Systems, methods, and devices for assessing microbiota of skin

ABSTRACT

Devices, systems, and methods for assessing microbiota of skin are described, including: a skin-covering material including an inner surface and an outer surface, the inner surface substantially conforming to a topography of a skin surface of an individual and including a plurality of signal-generating complexes, one or more of the plurality of signal-generating complexes configured to emit one or more signals in response to at least one type of microbe; an image capture device to capture an image of the inner surface of the skin-covering material, the image including one or more signals emitted from the plurality of signal-generating complexes, and to transform the image into a digital output; and a computing device including circuitry configured to receive the digital output, compare the properties of the imaged one or more signals with a database of reference signal-generating complexes, and generate a digital spatial profile of microbes on the skin-covering material.

If an Application Data Sheet (ADS) has been filed on the filing date ofthis application, it is incorporated by reference herein. Anyapplications claimed on the ADS for priority under 35 U.S.C. §§ 119,120, 121, or 365(c), and any and all parent, grandparent,great-grandparent, etc. applications of such applications, are alsoincorporated by reference, including any priority claims made in thoseapplications and any material incorporated by reference, to the extentsuch subject matter is not inconsistent herewith.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of the earliest availableeffective filing date(s) from the following listed application(s) (the“Priority Applications”), if any, listed below (e.g., claims earliestavailable priority dates for other than provisional patent applicationsor claims benefits under 35 USC § 119(e) for provisional patentapplications, for any and all parent, grandparent, great-grandparent,etc. applications of the Priority Application(s)). In addition, thepresent application is related to the “Related Applications,” if any,listed below.

PRIORITY APPLICATIONS

The present application constitutes a continuation of U.S. patentapplication Ser. No. 15/366,811, entitled SYSTEMS, METHODS, AND DEVICESFOR ASSESSING MICROBIOTA OF SKIN, naming Mahalaxmi G. Bangera, MichaelH. Baym, Roderick A. Hyde, Jordin T. Kare, Eric C. Leuthardt, Gary L.McKnight, Tony S. Pan, Katherine E. Sharadin, Elizabeth A. Sweeney,Clarence T. Tegreene, and Lowell L. Wood, Jr. as inventors, filed 1 Dec.2016 with attorney docket no. 0912-002-010-000001, which is currentlyco-pending or is an application of which a currently co-pendingapplication is entitled to the benefit of the filing date, and which isa continuation of U.S. patent application Ser. No. 13/975,079, entitledSYSTEMS, METHODS AND DEVICES FOR ASSESSING MICROBIOTA OF SKIN, namingMahalaxmi G. Bangera, Michael H. Baym, Roderick A. Hyde, Jordin T. Kare,Eric C. Leuthardt, Gary L. McKnight, Tony S. Pan, Katherine E. Sharadin,Elizabeth A. Sweeney, Clarence T. Tegreene, and Lowell L. Wood, Jr. asinventors, filed 23 Aug. 2013 with attorney docket no.0912-002-010-000000.

RELATED APPLICATIONS

U.S. patent application Ser. No. 13/975,055, now U.S. Pat. No.9,390,312, entitled SYSTEMS, METHODS, AND DEVICES FOR ASSESSINGMICROBIOTA OF SKIN, naming Mahalaxmi G. Bangera, Michael H. Baym,Roderick A. Hyde, Jordin T. Kare, Eric C. Leuthardt, Gary L. McKnight,Tony S. Pan, Katherine E. Sharadin, Elizabeth A. Sweeney, Clarence T.Tegreene, and Lowell L. Wood, Jr. as inventors, filed 23 Aug. 2013 withattorney docket no. 0912-002-005-000000, is related to the presentapplication.

U.S. patent application Ser. No. 13/975,067, now U.S. Pat. No.9,456,777, entitled SYSTEMS, METHODS, AND DEVICES FOR ASSESSINGMICROBIOTA OF SKIN, naming Mahalaxmi G. Bangera, Michael H. Baym,Roderick A. Hyde, Jordin T. Kare, Eric C. Leuthardt, Gary L. McKnight,Tony S. Pan, Katherine E. Sharadin, Elizabeth A. Sweeney, Clarence T.Tegreene, and Lowell L. Wood, Jr. as inventors, filed 23 Aug. 2013 withattorney docket no. 0912-002-009-000000, is related to the presentapplication.

If the listings of applications provided above are inconsistent with thelistings provided via an ADS, it is the intent of the Applicant to claimpriority to each application that appears in the Priority Applicationssection of the ADS and to each application that appears in the PriorityApplications section of this application.

All subject matter of the Priority Applications and the RelatedApplications and of any and all parent, grandparent, great-grandparent,etc. applications of the Priority Applications and the RelatedApplications, including any priority claims, is incorporated herein byreference to the extent such subject matter is not inconsistentherewith.

SUMMARY

In an aspect, a device for assessing microbiota of skin includes, but isnot limited to, a skin-covering material including an inner surface andan outer surface, the inner surface substantially conforming in shape toa topography of a skin surface of an individual and including attachedthereto a plurality of signal-generating complexes, each of theplurality of signal-generating complexes including at least onesignal-generating element and at least one specific microbe-bindingelement. In addition to the foregoing, other device aspects aredescribed in the claims, drawings, and text forming a part of thepresent disclosure.

In an aspect, a system for assessing microbiota of skin includes, but isnot limited to, a skin-covering material including an inner surface andan outer surface, the inner surface of the skin-covering materialsubstantially conforming in shape to a topography of a skin surface ofan individual and including attached thereto a plurality ofsignal-generating complexes, one or more of the plurality ofsignal-generating complexes configured to emit one or more signals inresponse to at least one type of microbe; an image-capture deviceincluding circuitry to capture at least one image of the inner surfaceof the skin-covering material, the at least one image including one ormore signals emitted from one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe and to transform the captured at least one image into a digitaloutput including information associated with at least one property and aspatial distribution of the imaged one or more signals; and a computingdevice including a processor, the computing device operably coupled tothe image-capture device and including circuitry configured to receivethe digital output from the image-capture device including theinformation associated with the at least one property and the spatialdistribution of imaged one or more signals emitted from the one or moreof the plurality of signal-generating complexes in response to the atleast one type of microbe; compare the properties of the imaged one ormore signals emitted from the one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe with a database of emitted signals of referencesignal-generating complexes; and generate a digital spatial profile ofthe at least one type of microbe based on the spatial distribution ofthe imaged one or more signals emitted from the one or more of theplurality of signal-generating complexes in response to the at least onetype of microbe. In addition to the foregoing, other system aspects aredescribed in the claims, drawings, and text forming a part of thepresent disclosure.

In an aspect, a method for assessing microbiota of skin includes, but isnot limited to, receiving a digital output from an image-capture device,the digital output including information associated with at least oneproperty and a spatial distribution of one or more signals emitted fromone or more of a plurality of signal-generating complexes associatedwith the inner surface of a skin-covering material, the one or moresignals emitted from the one or more of the plurality ofsignal-generating complexes in response to at least one type of microbe;identifying the at least one type of microbe by comparing theinformation associated with the at least one property of the one or moresignals emitted from the one or more of the plurality ofsignal-generating complexes with a database of single properties ofreference signal-generating complexes; generating a digital spatialprofile of the at least one type of microbe based on the spatialdistribution of the one or more signals emitted from the one or more ofthe plurality of signal-generating complexes; and reporting to a user anidentification and the digital spatial profile of the identified atleast one type of microbe. In addition to the foregoing, other methodaspects are described in the claims, drawings, and text forming a partof the present disclosure.

In an aspect, a method for assessing microbiota of skin includes, but isnot limited to, receiving a first digital output from an image-capturedevice, the first digital output including information associated withat least one property and a spatial distribution of a first set of oneor more signals emitted at a first time point from at least one of aplurality of signal-generating complexes associated with an innersurface of a first skin-covering material; receiving a second digitaloutput from the image-capture device, the second digital outputincluding information associated with at least one property and aspatial distribution of a second set of one or more signals emitted at asecond time point from at least one of a plurality of signal-generatingcomplexes associated with an inner surface of a second skin-coveringmaterial; comparing the first digital output with the second digitaloutput; generating a recommended treatment regimen based on thecomparison of the first digital output and the second digital output;and reporting the recommended treatment regimen to a user. In additionto the foregoing, other method aspects are described in the claims,drawings, and text forming a part of the present disclosure.

In an aspect, a method for assessing microbiota of skin includes, but isnot limited to, applying a skin-covering material to a skin surface ofan individual, the skin-covering material including an inner surface andan outer surface, the inner surface substantially conforming in shape toa topography of the skin surface of the individual and includingattached thereto a plurality of signal-generating complexes, one or moreof the plurality of signal-generating complexes configured to emit oneor more signals in response to at least one type of microbe; removingthe skin-covering material from the skin surface of the individual;capturing at least one image of the inner surface of the skin-coveringmaterial with an image-capture device, the at least one image includingone or more signals emitted from the one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe and transforming the captured at least one image into a digitaloutput including information associated with at least one property and aspatial distribution of the imaged one or more signals; receiving thedigital output from the image-capture device, the digital outputincluding the information associated with the at least one property andthe spatial distribution of the imaged one or more signals emitted fromthe one or more of the plurality of signal-generating complexes inresponse to the at least on type of microbe; identifying the at leastone type of microbe by comparing the information associated with the atleast one property of the imaged one or more signals emitted from theone or more of the plurality of signal-generating complexes with adatabase of signal properties of reference signal-generating complexes;generating a digital spatial profile of the at least one type of microbebased on the spatial distribution of the imaged one or more signalsemitted from the one or more of the plurality of signal-generatingcomplexes; and reporting to a user an identification and the digitalspatial profile of the identified at least one type of microbe. Inaddition to the foregoing, addition method aspects are described in theclaims, drawings, and text forming a part of the present disclosure.

In an aspect, an article of manufacture includes, but is not limited to:non-transitory machine readable media bearing one or more instructionsfor assessing microbiota of skin, the one or more instructions includingone or more instructions for receiving a digital output from animage-capture device, the digital output including informationassociated with at least one property and a spatial distribution of oneor more signals emitted from one or more of a plurality ofsignal-generating complexes associated with an inner surface of askin-covering material, the one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to atleast one type of microbe; one or more instructions for comparing theinformation associated with at least one property of the one or moresignals emitted from the one or more of a plurality of signal-generatingcomplexes with a database of signal properties of referencesignal-generating complexes; one or more instructions for generating amicrobe profile including the at least one property and the spatialdistribution of the one or more signals emitted from the one or more ofthe plurality of signal-generating complexes; instructions forgenerating a recommended treatment regimen for an individual based on acomparison of the microbe profile with a reference microbe profile; andone or more instructions for reporting to a user at least one of themicrobe profile or the recommended treatment regimen. In addition to theforegoing, other aspects of the article of manufacture are described inthe claims, drawings, and text forming a part of the present disclosure.

In an aspect, a system for assessing microbiota of skin includes, but isnot limited to, an image-capture device including circuitry to captureat least one image of an inner surface of a skin-covering material, theat least one image including one or more signals emitted from one ormore of a plurality of signal-generating complexes associated with theinner-surface of the skin-covering material in response to at least onetype of microbe and to transform the captured at least one image into adigital output including information associated with at least oneproperty and a spatial distribution of the imaged one or more signals; acomputing device including a processor, the computing device operablycoupled to the image-capture device; and non-transitory machine readablemedia readable by the computing device and bearing one or moreinstructions for assessing microbiota of skin, the one or moreinstructions including one or more instructions for receiving thedigital output from the image-capture device, the digital outputincluding the information associated with the at least one property andthe spatial distribution of the imaged one or more signals emitted fromthe one or more of a plurality of signal-generating complexes inresponse to the at least one type of microbe; one or more instructionsfor comparing the information associated with the at least one propertyof the imaged one or more signals emitted from the one or more of aplurality of signal-generating complexes with a database of signalproperties of reference signal-generating complexes; one or moreinstructions for generating a microbe profile including the at least oneproperty and the spatial distribution of the imaged one or more signalsemitted from the one or more of the plurality of signal-generatingcomplexes; instructions for generating a recommended treatment regimenfor an individual based on a comparison of the microbe profile with areference microbe profile; and one or more instructions for reporting toa user at least one of the microbe profile or the recommended treatmentregimen. In addition to the foregoing, other aspects of the article ofmanufacture are described in the claims, drawings, and text forming apart of the present disclosure.

The foregoing summary is illustrative only and is not intended to be inany way limiting. In addition to the illustrative aspects, embodiments,and features described above, further aspects, embodiments, and featureswill become apparent by reference to the drawings and the followingdetailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 includes FIGS. 1A and 1B illustrating an embodiment of askin-covering material.

FIG. 1A is a cross-section through a skin-covering material including aplurality of signal-generating complexes.

FIG. 1B illustrates a skin-covering material on an individual.

FIG. 2 includes FIGS. 2A-2C illustrating an embodiment of askin-covering material.

FIG. 2A is a cross-section through a peelable skin-covering materialincluding a plurality of signal-generating elements.

FIG. 2B illustrates a settable material of a skin surface.

FIG. 2C illustrates a peelable skin-covering material on individual.

FIG. 3 is a cross-section through a skin-covering material including aplurality of signal-generating complexes.

FIG. 4 is a cross-section through a skin-covering material including aplurality of signal-generating complexes.

FIG. 5 includes FIGS. 5A-5C illustrating an embodiment of askin-covering material.

FIG. 5A illustrates application of a peelable skin-covering materialincluding a plurality of signal-generating complexes to a skin surface.

FIG. 5B shows a cross-section through a peelable skin-covering materialincluding a plurality of signal-generating complexes on a skin surface

FIG. 5C illustrates a cross-section through a peelable skin-coveringmaterial including a plurality of signal-generating complexes.

FIG. 6 includes FIGS. 6A-6C showing an embodiment of a skin-coveringmaterial.

FIG. 6A illustrates application of a peelable skin-covering materialincluding a plurality of signal-generating complexes to a skin surface.

FIG. 6B shows a cross-section through a peelable skin-covering materialincluding a plurality of signal-generating complexes on a skin surface

FIG. 6C illustrates a cross-section through a peelable skin-coveringmaterial including a plurality of signal-generating complexes.

FIG. 7 is a schematic of a system including a skin-covering material forassessing microbiota of skin.

FIG. 8 illustrates aspects of a computing device.

FIG. 9 is a schematic of a system including a skin-covering material forassessing microbiota of skin.

FIG. 10 is a schematic of a system including a skin-covering materialfor assessing microbiota of skin.

FIG. 11 is a schematic of a system including a peelable skin-coveringmaterial for assessing microbiota of skin.

FIG. 12 includes FIGS. 12A-12C illustrating an embodiment of a systemincluding a skin-covering material.

FIG. 12A illustrates application of a peelable skin-covering material toa skin surface.

FIG. 12B shows a cross-section through a peelable skin-covering materialon a skin surface

FIG. 12C illustrates analysis of a peelable skin-covering material withan image-capture device.

FIG. 13 is a flowchart of a method for assessing microbiota of skin.

FIG. 14 is a flowchart illustrating further aspects of a method such asshown in FIG. 13.

FIG. 15 is a flowchart showing further aspects of a method such asdepicted in FIG. 13.

FIG. 16 is a flowchart of a method for assessing microbiota of skin.

FIG. 17 is a flowchart of a method for assessing microbiota of skin.

FIG. 18 is a flowchart illustrating further aspects of a method such asshown in FIG. 17.

FIG. 19 includes FIGS. 19A-19D showing an embodiment of a method such asshown in FIG. 17.

FIG. 19A illustrates further aspects of a method such as shown in FIG.17.

FIG. 19B shows further aspects of a method such as depicted in FIG. 17.

FIG. 19C depicts further aspects of a method such as illustrated in FIG.17.

FIG. 19D illustrates further aspects of a method such as shown in FIG.17.

FIG. 20 is a flowchart illustrating further aspects of a method such asshown in FIG. 17.

FIG. 21 includes FIGS. 21A-21C showing an embodiment of a skin-coveringmaterial.

FIG. 21A is a skin-covering material with lines of tearableperforations.

FIG. 21B is a skin-covering material with lines of tearableperforations.

FIG. 21C is a schematic of a system including a skin-covering materialwith lines of tearable perforations.

FIG. 22 is a schematic of a system including a mouthpiece for assessingmicrobiota of a mouth region.

FIG. 23 illustrates aspects of an article of manufacture for assessingmicrobiota of skin.

DETAILED DESCRIPTION

In the following detailed description, reference is made to theaccompanying drawings, which form a part hereof. In the drawings,similar symbols typically identify similar components, unless contextdictates otherwise. The illustrative embodiments described in thedetailed description, drawings, and claims are not meant to be limiting.Other embodiments may be utilized, and other changes may be made,without departing from the spirit or scope of the subject matterpresented here.

The skin, the largest organ of the mammalian body, is inhabited by adiverse array of microbes, including bacteria, fungi, viruses,parasites, archaea, or small arthropods (e.g., mites). Variations inregional properties of the skin, e.g., variations in pH, moisture,pores, texture, and the like, from one body location to anothercontribute to the spatial diversity of skin-associated microbes.Similarly, the type of microbes and/or spatial distribution of one ormore microbes on the skin surface may change in response to cleaning ofthe skin surface, application of anti-microbial agents, application ofirritating agents, e.g., make-up, lotion, sun screen, or exposure toirritating conditions, e.g., diet, disease, wind, or sun exposure. Insome instances, skin-resident microbes on the skin surface, e.g.,commensal bacteria, provide a benefit to the individual. For example,Staphylococcus epidermidis has been demonstrated to modulate the hostinnate immune response, inhibiting other bacterial pathogens such asStaphylococcus aureus and Group A Streptococcus. See, e.g., Grice &Segre (2011) Nat. Rev. Microbiol. 9:244-53, which is incorporated hereinby reference. In some instances, skin-resident microbes have been linkedto pathological conditions including acne, psoriasis, and atopicdermatitis. See, e.g., Cho & Blaser (2012) Nat. Rev. Genet. 13:260-270,which is incorporated herein by reference. In general, understanding theidentity and spatial distribution of skin-resident microbes on the skinunder normal and/or pathological conditions can contribute to decisionsregarding therapeutic, preventative, and/or cosmetic treatments.Described here are embodiments of systems, methods, and devices forassessing the microbiota of skin.

FIGS. 1A and 1B illustrate a device 100 for assessing microbiota ofskin. FIG. 1A is a schematic cross-section through device 100. Device100 includes skin-covering material 110 with inner surface 120 and outersurface 130. Inner surface 120 substantially conforms in shape to atopography of skin surface 140 of individual 150. Inner surface 120further includes attached thereto a plurality of signal-generatingcomplexes 160. Each of the plurality of signal-generating complexes 160includes at least one signal-generating element and at least onespecific microbe-binding element.

In an aspect, at least one of the plurality of signal-generatingcomplexes 160 is configured to emit one or more signals in response toat least one type of microbe. In an aspect, the plurality ofsignal-generating complexes associated with the inner surface of theskin-covering material come into contact with at least one type ofmicrobe when the skin-covering material is placed on the skin surface ofan individual. In an aspect, the at least one type of microbe caninclude at least one type of mutualistic microbe, commensal microbe, orpathogenic microbe. In an aspect, the at least one type of microbeincludes at least one type of skin-associated or skin-resident bacteria.The at least one type of microbe includes at least one type of bacteria,fungus, virus, parasite, archaea, or small arthropod (e.g., mites). Inan aspect, the at least one type of microbe includes at least one typeof mutualistic microbe, commensal microbe, or pathogenic microbe. In anaspect, the at least one type of microbe captured by the skin-coveringmaterial can include at least one type of skin-resident microbe.Non-limiting examples of skin-associated or skin-resident bacteriainclude proteobacteria, e.g., Pseudomonas sp., Janthinobacterium sp,Alphaproteobacteria, other gammaproteobacteria, and betaproteobacteria;Actinobacteria, e.g., Kocuria sp., Propionibacteria sp.; Firmicutes,e.g., Staphylococcus epidermidis; Bacteroidetes; and Spirochaetes. See,e.g., Grice et al. (2008) Genome Res. 18:1043-1050; Grice & Segre (2011)Nat. Rev. Microbiol. 9:244-253, which are incorporated herein byreference. Non-limiting examples of fungi, including skin-resident orassociated types of fungi, include dermatophtyes, e.g., trichophyton,microsporum, epidermophyton, tinea capitis. Other skin associated fungiinclude but are not limited to yeast, Candida, e.g., Candida albicans;and Malassezia spp (e.g., M. dermatis, M. furfur, M. globosa, and M.restricta). See, e.g., Gaitanis et al. (2012) Clin. Microbiol. Rev.25:106-141, which is incorporated herein by reference. Non-limitingexamples of skin-associated or skin-resident viruses include herpessimplex virus type I (HSV-1), herpes zoster, Molluscum contagiosum,human papillomavirus (HPV), Coxsackie virus A16, and herpes gladiatorum.Non-limiting examples of other parasites resident or associated with askin surface include skin-associated parasitic arthropods includingparasitic mites, e.g., Demodex spp including D. folliculorum and D.brevis, and Sarcoptes scabiei, a skin parasite associated with scabies.

In an aspect, at least one of the plurality of signal-generatingcomplexes is configured to emit one or more signals upon interactionwith at least one type of microbe. In an aspect, the interaction withthe at least one type of microbe is a binding interaction, in which theat least one type of microbe binds to a portion of the signal-generatingcomplex and induces emission of a signal. In an aspect, the microbe maybe physically attached to the signal-generating complex. In an aspect, abrief interaction between the microbe and the signal-generating complexmay be sufficient to induce a signal. In an aspect, the interaction ofthe signal-generating complex with the at least one type of microbe is achemical interaction, in which some component of the microbe, e.g., anexcreted component, interacts with the signal-generating complex toinduce emission of a signal.

FIG. 1B illustrates device 100 on the skin surface of individual 150. Inthis instance, the inner surface of device 100 substantially conforms tothe topography of the face of individual 150, but may be configured foruse on any of a number of skin surfaces of an individual. In an aspect,inner surface 120 of skin-covering material 110 substantially conformsin shape to a topography of a skin surface of an individual. Thetopography of the skin surface can include both the micro-topography,e.g., the texture and/or pattern of the skin surface, and themacro-topography, e.g., anatomical features such as nose, lips, cheeks,large wrinkles, joints, and the like. The skin surface can include anyof a number of regions of the body including, but not limited to thefacial region, torso region, abdominal region, head region, neck region,upper extremity, lower extremity, buttocks, or any other body region forwhich analysis of the spatial distribution of microbiota of theindividual is desired. In an aspect, skin-covering materialsubstantially conforms in shape to a topography of one or more surfacesof a mouth region of an individual. The one or more surfaces of themouth region of the individual can include one or more of an oralmucosa, a tooth, gingiva, tongue, and/or palate. In an aspect, innersurface 120 of skin-covering material 110 may be configured tosubstantially conform in shape to the topography of the skin surface ofall or part of the individual's face to form, for example, a mask-likecovering. In an aspect, the skin-covering material is personalized tosubstantially conform to the topography of the skin surface of aspecific individual. In an aspect, the skin-covering material isnon-planar, e.g., substantially conforming in shape to a topography of askin surface that includes non-planar contours, e.g., the features of aface.

In an aspect, skin-covering material 110 includes a pre-formedskin-covering. In an aspect, the pre-formed skin-covering materialincludes a semi-rigid pre-formed skin-covering material. For example,the skin-covering material can include a thin flexible substrate thatconforms to the topography of the skin surface of the individual. Forexample, the skin-covering material can include a flexible strip, awrap, a band, or the like that conforms to the curvature of a skinsurface, e.g., the curvature of the face or arm pit or around anextremity, making uniform contact with the skin so as to uniformlycapture representative microbes from all portions of the covered skin.For example, the semi-rigid pre-formed skin-covering material mayinclude a specially coated strip of bendable material, e.g., a coatedsheet of Mylar or a treated piece of fabric, that when applied to a skinsurface substantially conforms in shape to the topography of the skinsurface, e.g., wraps around the contours of a body part. In an aspect,the skin-covering material includes a flexible strip similar to a woundcovering but with a region configured to capture one or moreskin-resident microbes.

In an aspect, the pre-formed skin-covering material includes a rigidpre-formed skin-covering material. For example, the rigid pre-formedskin-covering material can include a rigid thin plastic substrate thathas been designed and manufactured, e.g., by three-dimensional printing,to substantially conform in shape to the topography of an individual'sskin surface. For example, the rigid pre-formed skin-covering materialcan include a mask-like structure that substantially conforms in shapeto the topography of the skin surface of an individual's face. Ingeneral, the pre-formed skin-covering material is configured tosubstantially conform to the topography of the skin surface of theindividual to achieve uniform contact of the microbe-capture region onthe inner surface of the skin-covering material with the underlying skinsurface.

In an aspect, the pre-formed skin-covering material includes a thinsubstrate that is non-planar and is either flexible or rigid. Forexample, the pre-formed skin-covering material may include a structurethat mirrors the contours and/or topography of a specific region of theskin. For example, the pre-formed skin-covering material may have anon-planar structure that mirrors the contours and/or topography of anindividual's face and as such when placed on the surface of the skinmakes uniform contact with substantially all of the overlappingportions. For example, the pre-formed skin-covering material can includea non-planar, flexible latex-like thin substrate that substantiallyconforms to the topography of the skin surface of the individual. Forexample, the pre-formed skin-covering material can include a non-planar,hard plastic-like, thin substrate that substantially conforms to thetopography of the skin surface of the individual. In an aspect, therigid or semi-rigid pre-formed skin-covering material is formed usingthree-dimensional printing to substantially conform to a digitalrendering of a skin surface topography of an individual. In an aspect,the rigid or semi-rigid pre-formed skin-covering material is generic,substantially conforming to the topography of the skin surface of any ofa number of individuals.

In an aspect, the pre-formed skin-covering material may cause thetopography of the skin to conform to the topography of the skin-coveringmaterial, e.g., when a pre-formed skin-covering material is pressed upona conformable body part, e.g., a body part including ample soft tissue.For example, a pre-formed rigid skin-covering material, e.g., a mask,may be pressed against an individual's cheek, buttocks, or upper thighto achieve uniform contact of the pre-formed skin-covering material withthe underlying skin surface.

The pre-formed skin-covering material can include any of a number ofmaterials capable of being shaped, molded or printed to form thepre-formed skin-covering material. Non-limiting examples of shapeable,moldable or printable materials include acrylic, nylon, plastic,ceramic, resin, rubber, epoxy, thermoplastic, polymer, photopolymer,polyurethane, gel, hydrogel, latex, or silicone. Additional non-limitingexamples of shapeable, moldable or printable materials for use informing the skin covering include: metals such as titanium/titaniumalloys, TiNi (shape memory/super elastic), aluminum oxide,platinum/platinum alloys, stainless steels, pyrolytic carbon, silver orglassy carbon; polymers such as polyurethanes, polycarbonates, siliconeelastomers, polyolefins including polyethylenes or polypropylenes,polyvinyl chlorides, polyethers, polyesters, nylons, polyvinylpyrrolidones, polyacrylates and polymethacrylates such aspolymethylmethacrylate (PMMA), n-Butyl cyanoacrylate, polyvinylalcohols, polyisoprenes, rubber, cellulosics, polyvinylidene fluoride(PVDF), polytetrafluoroethylene, ethylene tetrafluoroethylene copolymer(ETFE), acrylonitrile butadiene ethylene, polyamide, polyimide, styreneacrylonitrile, and the like; minerals or ceramics such as hydroxapatite;organic materials such as wood, cellulose, or compressed carbon; andother materials such as glass, or the like.

The pre-formed skin-covering material may be formed from shapeable,moldable, or printable materials by a variety of manufacturing methods.In some embodiments, the pre-formed skin-covering material is generatedfrom a mold made of a skin surface of the individual. For example, amold of a skin surface of an individual can be generated by covering theskin surface, e.g., an individual's face, with a material that hardensto conform in shape to a topography of the skin surface. For example,alginate may be used in combination with plaster bandages to create amold of a skin surface of an individual, e.g., the individual's face. Insome embodiments, the mold itself can be used as the pre-formedskin-covering material. Non-limiting examples of materials that can beused for generating a mold of a skin surface of an individual includemodeling clay, plaster, alginate, or combinations thereof. In someembodiments, the mold can be a reusable template for forming one or morepre-formed skin-covering material with a material, e.g., latex, that ispoured or spread into the mold, hardened, and removed from the mold.

In an aspect, the pre-formed skin-covering material is personalized tosubstantially conform to the topography of the skin surface of theindividual. For example, a digital three-dimensional representation ofthe skin surface of the individual may be used to digitally render apre-formed skin-covering, the latter of which is used as a template formanufacturing the pre-formed skin-covering using a three-dimensionalprinter. One or more digital images of the skin surface of theindividual for use in generating a digital three-dimensionalrepresentation of the skin surface can be acquired from one or more of adigital camera or scanning device. For example, two video cameras,slightly apart, can be used to image the same portion of skin surface ofthe individual in a process termed stereophotogrammetry. For example, asingle camera can be used to take multiple images under differentlighting conditions or from different positions. In an aspect, thetopography of the skin surface of an individual can be acquired in apoint-cloud format using a three-dimensional sensing system consistingof two or more digital cameras and one or more projectors connected to apersonal computer. The camera position and shutter can be adjusted tothe body region, which is exposed to structured light, allowing foroptical representation of the surface by a cloud of up to 300,000 pointsin three-dimensional coordinates (see, e.g., Feng et al., Br. J. OralMaxillofac. Surg. (2010) 48:105-109, which is incorporated herein byreference). In some embodiments, the combination of stereophotogrammetryand 3D laser scanner techniques can be combined to generate athree-dimensional model of the skin surface of an individual (see, e.g.,Majid, et al. International Archives of the Photogrammetry, RemoteSensing and Spatial Information Science. Vol. XXXVII. Part B5. (2008)805-811; Markiewicz & Bell, Facial Plast. Surg. Clin. N. Am. (2011)19:655-682; van Heerbeek et al., Rhinology (2009) 47:121-125, which areincorporated herein by reference). Scanners for scanning head, faceand/or whole body are commercially available (from, e.g., Cyberware,Monterery Calif.; Accurex Measurement Inc., Swathmore, Pa.; 3dMDAtlanta, Ga.; Konica/Minolta, Ramsey, N.J.)

In an aspect, surface scanning software can be used to import individualpoints of the skin surface, e.g., of the face, and then combine them inthe X, Y, and Z axes to render a three-dimensional representation of thetopography of the skin surface. In some embodiments, the one or moreimages of the skin surface may include point clouds of data that arereconstructed using one or more three-dimensional modeling algorithms toform a digitally rendered model of the skin-covering material. One ormore modeling programs can be used for this purpose. Non-limitingexamples of types of modeling programs include polygonal meshthree-dimensional modeling programs, non-uniform rational basis spline(NURBS) surface modeling programs, or editable feature-based computeraided design (CAD) modeling programs. In some embodiments, the data maybe modeled using a first modeling approach, for example, a NURBS basedmodeling program and further refined using a second modeling approach,for example, a CAD-based modeling program. Numerous software programsare available for generating three-dimensional models from scannedimages. For example, non-limiting examples of CAD/CAM software programsapplicable to medical imaging include Amira (Visage Imaging GmbH, BerlinGermany); Analyze (AnalyzeDirect, Inc, Overland Park, Kans.); iNtellectCranial Navigation System (Stryker, Freiburg, Germany); iPlan (BrainLab,Westchester, Ill.); Maxilim (Medicim, Bruges Belgium), Mimics, SurgiCaseCMF, and SimPlant OMS (Materialise, Leuven, Belgium); Voxim (IVSSolutions, Chemnitz, Germany), 3dMD (Atlanta, Ga.); Alma3D (Alma ITSystems, Barcelona, Spain); and ImageJ (National Institutes of Health,Boston, Mass.) (see, e.g., Markiewicz & Bell, Facial Plast. Surg. Clin.N. Am. (2011) 19:655-682, which is incorporated herein by reference).Facial feature extraction can be acquired using one or more of an activeshape model algorithm (see, e.g., Sun & Xie, 11^(th) IEEE InternationalConference on Communication Technology Proceedings, (2008) pp. 661-664;Zheng & Yang IEEE Proceedings of the Seventh International conference onMachine Learning and Cybernetics, (2008) pp. 2841-2845, which areincorporated herein by reference). Other software packages capable ofgenerating a digitally rendered model of the skin-covering material fromone or more digital images of a skin surface of an individual can beused for this purpose. Additional approaches for generatingthree-dimensional models are described in Bernardini & RushmeierComputer Graphics Forum (2002) 21:149-172, which is incorporated hereinby reference.

In an aspect, information regarding the digitally rendered model of thepre-formed skin-covering material is sent to a manufacturing devicewhich produces the pre-formed skin-covering material based on thereceived information. Non-limiting examples of methods for generating athree-dimensional structure from digitized information includestereolithography, laser sintering, fused deposition modeling, polyj et,three-dimensional printing, vacuum casting, reaction injection molding,or injection molding. Non-limiting examples of materials for generatinga three-dimensional structure from digitized information include one ormore of acrylic, nylon, plastic, ceramic, resin, rubber, epoxy,thermoplastic, photopolymer, polyurethane, latex or silicone. The typeof material used for forming the pre-formed skin-covering material isdependent upon the method used to form the pre-formed skin-coveringmaterial and the desired properties, e.g., rigidity, transparency,and/or porosity, of the final product. Exemplary materials and methodsfor forming a pre-formed skin-covering material using stereolithography,laser scintering or three-dimensional printing as well as other methodsfor forming a pre-formed skin-covering material from the digitallyrendered model of the pre-formed skin-covering material are describedherein.

In an aspect, the pre-formed skin-covering material is formed using anadditive manufacturing process. Additive manufacturing refers to a classof manufacturing process in which a three-dimensional object is built byadding layers of material upon one another. Other terms include layeredmanufacturing, direct digital manufacturing, or solid freeformfabrication. Non-limiting examples of additive manufacturing processesinclude liquid-based processes, e.g., stereolithography, jettedphotopolymer, and ink jet printing; powder-based processes, e.g.,selective laser sintering, direct metal laser sintering, andthree-dimensional printing; and solid-based processes, e.g., laminatedobject manufacturing, fused deposition modeling.

In an aspect, the pre-formed skin-covering material is formed using asubtractive manufacturing process. Subtractive manufacturing refers to aclass of manufacturing process in which a three-dimensional object isbuilt by cutting away material. Non-limiting examples of subtractivemanufacturing processes include machining, milling, turning, anddrilling. Other non-limiting examples of manufacturing processes includemolding, e.g., blow molding, injection molding, or thermoforming; andcasting, e.g., centrifugal casting, die casting, sand casting, shellmold casting.

In an aspect, the pre-formed skin-covering material is generated usingstereolithography using one or more optically curable photopolymers.Non-limiting examples of materials useful for stereolithography includepoly(ethylene glycol) 1500, Accura 60, Accura 25, Accura Xtreme, Somos9420, Somos 11122, Somos 18420, Somos DMX, Rigi2200,TuskXC2700T/Tusk2700 W, Nano5000, Flex45, Flex65, Flex70B, Flex 80,Protogen White. Other non-limiting examples of stereolithography includethree-dimensional printing (3D printing), optical fabrication,photo-solidification, solid free-form fabrication, and solid imaging.

In an aspect, the pre-formed skin-covering material can be generated by3D printing using an inkjet technology, e.g., PolyJet™ (from Objet Ltd)in which photopolymer materials are jetted in ultra-thin layers onto abuild tray and cured layer by layer with UV light. Non-limiting examplesof materials for use in generating a pre-formed skin-covering materialusing inkjet technology include Fullcure 720, VeroWhite, VeroBlack,VeroBlue, and VeroGray for rigid structures; Durus for semi-flexiblestructures; and Tango Elastomers for rubber-like structures. Otherexamples of 3D printers include ProJet and ZPrinters available from 3DSystems Corporation, Rock Hill S.C. and Freeform Pico, Asiga, AnaheimHills, Calif.

In an aspect, the pre-formed skin-covering material is generated usingselective laser sintering in which a high power laser, e.g., a carbondioxide laser, is used to fuse small particles of plastic, metal,ceramic, glass powders, or combinations thereof into a mass that has adesired three-dimensional shape. Non-limiting examples of material foruse in generating a pre-formed skin-covering material guide using lasersintering include polyamide, nylon, carbon, hydroxyapatite, glass filledpolyamide, and alumide.

In an aspect, the pre-formed skin-covering material is generated usingfused deposition modeling. Fused deposition modeling is an extrusionbased three-dimensional modeling process using thermoplastic materials.Non-limiting examples of materials for use in fused deposition modelinginclude the thermoplastics ABS, ABS/F1, polycarbonate, and Ultem 9085.The uPrint SE from Stratasys (Eden Prairie, Minn.) or the DimensionElite 3D printer from Dimension, Inc. (Eden Prairie, Minn.) arenon-limiting examples of systems for fused deposition modeling withthermoplastics that might be appropriate for use in a medical clinic.

In an aspect, the pre-formed skin-covering material can be formed from athree-dimensional mold surface formed from the digitally rendered modelof the pre-formed skin-covering material and using the three-dimensionalmold surface with a moldable material to generate the pre-formedskin-covering material. For example, a three-dimensional mold surface ofthe individual's face can be fabricated from a thermoplastic materialbased on the digitally rendered model of the wearable injection guide. Amoldable material, e.g., latex, can then be poured into or over thethree-dimensional mold surface to generate the formed pre-formedskin-covering material. The three-dimensional mold surface can be usedrepeatedly to generate one or more pre-formed skin-covering material.

In an aspect, the skin-covering material can include a peelableskin-covering material. FIG. 2 illustrates aspects of a device 200including a peelable skin-covering material. FIG. 2A is a schematiccross-section through device 200. Device 200 includes peelableskin-covering material 210 which includes inner surface 220 and outersurface 230. Inner surface 220 substantially conforms in shape to thetopography of skin surface 240 of individual 250. Inner surface 220further includes attached there to a plurality of signal-generatingcomplexes 260. In this non-limiting example, signal-generating complexes260 are integrated throughout peelable skin-covering material 210.

In an aspect, peelable skin-covering material 210 includes a flexiblesolid, the flexible solid including the plurality of signal-generatingcomplexes. The peelable skin-covering material can include any of anumber of materials applied to the skin surface of the individual andsubsequently peeled as a single piece from the surface of the skin. Forexample, the peelable skin-covering material can include one or moreshapeable or moldable materials applied to the skin surface of anindividual and peeled therefrom. In some embodiments, the shapeable ormoldable material may harden over an elapsed period of time or byexposure to ambient air. In some embodiments, the shapeable or moldablematerial may be hardened in response to electromagnetic energy, e.g.,light of a specific wavelength, or in response to elevated temperature.

In an aspect, peelable skin-covering material 210 includes a settablematerial, the settable material including a plurality ofsignal-generating complexes. FIG. 2B illustrates settable material 270including plurality of signal-generating complexes applied to skinsurface 240 of individual 250. Settable material 270 can include atleast one material configured to undergo a phase change from a liquid orgelled phase to a flexible solid phase in response to an appliedstimulus. For example, the settable material can include a material thatis poured onto the skin surface of an individual. For example, thesettable material can include a material that is spread onto the skinsurface of an individual. Non-limiting examples of settable materialinclude latex, gel, polymer, plastic, or resin. For example, thesettable material can include one or more polymers, e.g., polyvinylalcohol, polyacrylate, polymethacrylate and/or polyacrylamide. See,e.g., U.S. Pat. No. 5,747,022; U.S. Patent Application 2005/0019291,which are incorporated herein by reference. The applied stimulus caninclude one or more of exposure to air, a thermal stimulus, e.g., heat,or an electromagnetic stimulus, e.g., exposure to a specific wavelengthor spectrum of light.

In an aspect, the peelable skin-covering material includes a shrink-wrapmaterial that is applied to the skin surface as a thin sheet andconformed in shape to the topography of the skin surface using anapplied stimulus, e.g., heat.

FIG. 2C shows peelable skin-covering material 210 on the skin surface ofindividual 250. In this non-limiting example, the inner surface ofpeelable skin-covering material 210 substantially conforms to thetopography of the face of individual 250, but may be configured for useon any of a number of skin surfaces of an individual as described aboveherein.

In an aspect, the plurality of signal-generating complexes areincorporated into the skin-covering material. In an aspect, theplurality of signal-generating complexes are substantially uniformlydistributed throughout the skin-covering material. For example, theplurality of signal-generating complexes may be uniformly dispersed in aliquid or gelled form during manufacture of the skin-covering materialas shown, for example, in FIG. 2.

In an aspect, at least a portion of the plurality of signal-generatingcomplexes are distributed along at least a portion of the inner surfaceof the skin-covering material. In an aspect, the plurality ofsignal-generating complexes are substantially uniformly distributed overat least a portion of the inner surface of the skin-covering material asshown, for example, in FIG. 1. In an aspect, at least a portion of theplurality of signal-generating complexes are functionally attached tothe inner surface of the skin-covering material. In an aspect, at leastone of the plurality of signal-generating complexes are covalentlyattached to the inner surface of the skin-covering material. In anaspect, at least one of the plurality of signal-generating complexes isnon-covalently attached to the inner surface of the skin-coveringmaterial.

In an aspect, one or more of the plurality of signal-generatingcomplexes are covalently attached to at least the inner surface of theskin-covering material using a crosslinking reagent. In an aspect, thecrosslinking reagent includes at least one of a homobifunctional,heterobifunctional, and/or photoreactive crosslinking reagent. Forexample, the inner surface of the skin-covering material may include alayer of silane to which is bound one arm of a heterobifunctionalcrosslinking reagent. See, e.g., U.S. Pat. No. 5,077,210, which isincorporated herein by reference. In an embodiment, the other arm of theheterobifunctional crosslinking reagent is covalently bound to asignal-generating complex. The one or more of the plurality ofsignal-generating complexes can be cross-linked to the inner surface ofthe skin-covering material through amine groups, carbohydrate groups,sulfhydryl groups, or combinations thereof. Non-limiting examples ofhomobifunctional crosslinking reagents include primary amine/primaryamine linkers such as BSOCES ((bis(2-[succinimidooxy-carbonyloxy]ethyl)sulfone), DMS (dimethyl suberimidate), DMP (dimethyl pimelimidate), DMA(dimethyl adipimidate), DSS (disuccinimidyl suberate), DST(disuccinimidyl tartate), Sulfo DST (sulfodisuccinimidyl tartate), DSP(dithiobis(succinimidyl propionate), DTSSP (3,3′-dithiobis(succinimidylpropionate), EGS (ethylene glycol bis(succinimidyl succinate)) andsulfhydryl/sulfhydryl linkers such as DPDPB(1,4-di-(3′-[2′pyridyldithio]-propionamido) butane). Non-limitingexamples of heterobifunctional crosslinking reagents include primaryamine/sulfhydryl linkers such as MBS(m-maleimidobenzoyl-N-hydroxysuccinimide ester), Sulfo MBS(m-maleimidobenzoyl-N-hydroxysulfosuccinimide), GMBS(N-gamma-maleimidobutyryl-oxysuccinimide ester), Sulfo GMBS(N-gamma-maleimidobutyryloxysulfosuccinimide ester), EMCS(N-(epsilon-maleimidocaproyloxy) succinimide ester), Sulfo EMCS(N-(epsilon-maleimidocaproyloxy) sulfo succinimide), SIAB(N-succinimidyl(4-iodoacetyl)aminobenzoate), SMCC (succinimidyl4-(N-maleimidomethyl) cyclohexane-1-carboxylate), SMPB (succinimidyl4-(rho-maleimidophenyl) butyrate), Sulfo SIAB(N-sulfosuccinimidyl(4-iodoacetyl)aminobenzoate), Sulfo SMCC(sulfosuccinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate),Sulfo SMPB (sulfosuccinimidyl 4-(rho-maleimidophenyl) butyrate), andMAL-PEG-NHS (maleimide PEG N-hydroxysuccinimide ester);sulfhydryl/hydroxyl linkers such as PMPI (N-rho-maleimidophenyl)isocyanate; sulfhydryl/carbohydrate linkers such as EMCH(N-(epsilon-maleimidocaproic acid) hydrazide); and amine/carboxyllinkers such as EDC (1-ethyl-3-(3-dimethylaminopropyl) carbodiimidehydrochloride).

In an aspect, one or more of the plurality of signal-generatingcomplexes are non-covalently attached to at least the inner surface ofthe skin-covering material. Non-limiting examples of non-covalentinteractions include hydrogen bonds, ionic bonds, van der Waals forces,and hydrophobic interactions. For example, a signal-generating complexthat includes an oligonucleotide could be non-covalently attached to acomplementary oligonucleotide incorporated into the inner surface of askin-covering material. In an aspect, the one or more of the pluralityof signal-generating complexes are non-covalently attached to the innersurface of the skin-covering material through protein-proteininteractions. For example, a signal-generating complex that includesbiotin could be non-covalently attached to an inner surface thatincludes streptavidin or avidin. For example, a single chain antibodymay incorporate streptavidin as part of a fusion protein to facilitateattachment of the antibody to a solid substrate via abiotin-streptavidin linkage. See, e.g., Koo et al. (1999) Appl. Environ.Microbiol. 64:2497-2502, which is incorporated herein by reference.Other non-limiting examples non-covalent interactions includeinteractions between protein A or protein G and immunoglobulins, ligandswith receptors, and secondary antibodies with primary antibodies.

In an aspect, the plurality of signal-generating complexes associatedwith the inner surface of the skin-covering material are configured toemit one or more signals in response to two or more types of microbes,each type of microbe associated with a unique signal emitted from one ormore of the plurality of signal-generating complexes. In an aspect, theplurality of signal generating complexes includes a plurality ofsignal-generating complexes of at least one first type and a pluralityof signal-generating complexes of at least one second type. In anaspect, the plurality of signal-generating elements of the at least onefirst type differ from the plurality of signal-generating elements ofthe at least one second type. In an aspect, the plurality of thesignal-generating complexes of the at least one first type emit one ormore signals of a first type in response to at least one first type ofmicrobe and the plurality of signal-generating complexes of the at leastone second type emit one or more signals of a second type in response toat least one second type of microbe. In an aspect, the at least onefirst type of microbe differs from the at least one second type ofmicrobe. For example, the at least one first type of microbe can includea different phylum from the at least one second type of microbe, e.g.,bacteria versus fungi. For example, the at least one first type ofmicrobe can include a different genus from the at least one second typeof microbe, e.g., Staphylococcus versus Propionibacterium. For example,the at least one first type of microbe can includes a different speciesfrom the at least one second type of microbe, e.g., Staphylococcusaureus versus Staphylococcus epidermidis. In an aspect, the one or moresignals of the first type differ from the one or more signals of thesecond type. For example, the one or more signals of the first type candiffer in wavelength, e.g., color, from the one or more signals for thesecond type. In an aspect, a specific color can be associated with aresponse to a specific microbe, e.g., a red signal associated withStaphylococcus and a green signal associated with Propionibacterium.

In an aspect, the skin-covering material includes at least oneregistration mark to register the skin-covering material to at least onelandmark on the skin surface of the individual. One or more registrationmarks on the skin-covering material can be used to align with one ormore landmarks on the skin surface. The one or more landmarks caninclude one or more of pigmentation, pigmented areas, tattoos, skintexture patterns, blemishes, scars, anatomical features, or subsurfaceblood vessels associated with the skin surface. In an aspect, the one ormore registration marks are incorporated into the manufacture of theskin-covering material based on a digital image of the skin surfaceincluding the one or more landmarks over which the skin-coveringmaterial will be placed. In an aspect, the one or more registrationmarks can be added with a pen or other marking device while theskin-covering material is on the skin surface of the individual.

In an aspect, the skin-covering material includes one or more tearablelines of perforations. In an aspect, the one or more tearable lines ofperforation are configured to allow separation of the skin-coveringmaterial into two or more segments. In an aspect, the skin-coveringmaterial can be manufactured with perforations. For example, theskin-covering material may be manufactured using a three-dimensionalprinting process as described herein in which the digital template forthe skin-covering material includes perforations. In an aspect, theperforations are added to the skin-covering material after manufacture.For example, a skin-covering material manufactured from a thin sheet ofmaterial, e.g., latex or paper may be modified with a device configuredto punch holes through the skin-covering material. In general, thetearable lines of perforations allow the skin-covering material to beseparated into pieces that can be accommodated by the imaging window orscanning surface of the image-capture device, the one or more resultingimages digitally recombined to form a composite image of the innersurface of the skin-covering material. In an aspect, the one or moretearable lines of perforations are configured to allow partialseparation of the skin-covering material. For example, the one or moretearable lines of perforations can be configured to allow partialseparation of portions of an otherwise non-planar skin-covering materialto be flattened, i.e., made planar, to facilitate imaging with an imagecapture device.

In an aspect, each of the plurality of signal-generating complexesincludes at least one signal-generating element and to at least onespecific microbe-binding element. In an aspect, the at least onesignal-generating element is operably coupled to the at least onespecific microbe-binding element, wherein the at least one signalgenerating element is configured to emit one or more signals in responseto at least one type of microbe bound to the operably coupled at leastone specific microbe-binding element. FIG. 3 is a schematiccross-section through device 300 for assessing microbiota of skin.Device 300 includes skin-covering material 310 with inner surface 320and outer surface 330. Inner surface 320 includes attached thereto aplurality of signal-generating complexes, each of the signal-generatingcomplexes including signal-generating element 340 and specificmicrobe-binding element 350. In an aspect, signal-generating element 340is operably coupled to specific microbe-binding element 350. Specificmicrobe-binding element 350 is configured to specifically recognize atleast one type of microbe. Signal-generating element 340 is configuredto emit one or more signals in response to at least one type of microbebound to the operably coupled specific microbe-binding element 350.

In an aspect, the skin-covering material includes a plurality ofsignal-generating elements of at least one first type including at leastone signal-generating element of a first type operably coupled to atleast one specific microbe-binding element of a first type, the at leastone signal-generating element of the first type to emit one or moresignals of a first type in response to at least one first type ofmicrobe bound to the operably coupled at least one specificmicrobe-binding element of the first type and a plurality ofsignal-generating complexes of at least one second type including atleast one signal-generating element of a second type operably coupled toat least one specific microbe-binding element of a second type, the atleast one signal-generating element of the second type to emit one ormore signals for a second type in response to at least one second typeof microbe bound to the operably coupled at least one specificmicrobe-binding element of the second type. In an aspect, the at leastone first type of microbe differs from the at least one second type ofmicrobe. In an aspect, the one or more signals of the first type differfrom the one or more signals of the second type.

FIG. 4 is a schematic cross-section through device 400 for assessingmicrobiota of skin and including a plurality of signalgenerating-complexes of a first type and a plurality ofsignal-generating complexes of a second type. Device 400 includesskin-covering material 410 with inner surface 420 and outer surface 430.Inner surface 420 includes attached thereto a plurality ofsignal-generating complexes of a first type including signal-generatingelement of a first type 440 and specific microbe-binding element of afirst type 450 and a plurality of signal-generating complexes of asecond type including signal-generating element of a second type 460 andspecific microbe-binding element of a second type 470. In an aspect,signal-generating element of a first type 440 is operably coupled to aspecific microbe-binding element of a first type 450 andsignal-generating element of a second type 460 is operably coupled to aspecific microbe-binding element of a second type 470. Specificmicrobe-binding element of a first type 450 recognizes at least onefirst type of microbe while specific microbe-binding element of a secondtype 470 recognizes at least one second type of microbe.Signal-generating element of a first type 440 is configured to emit oneor more signals of a first type in response to the at least one firsttype of microbe bound to operably coupled specific microbe-bindingelement of a first type 450 and signal-generating element of a secondtype 460 is configured to emit one or more signals of a second type inresponse to the at least one second type of microbe bound to operablycoupled specific microbe-binding element of a second type 470.

In an aspect, a given type of signal-generating element is operablycoupled to a given type of specific microbe-binding element to provide amicrobe-specific signal. For example, a first signal-generating elementemitting light at a first wavelength band, e.g., red fluorescence, maybe operably coupled to a first type of specific microbe-binding elementthat binds a first type of microbe while a second signal-generatingelement emitting light at a second wavelength band, e.g., greenfluorescence, may be operably coupled to a second type of specificmicrobe-binding element that binds a second type of microbe, allowingfor distinct detection of the first type of microbe versus the secondtype of microbe.

FIG. 5 is a schematic cross-section through a peelable skin-coveringmaterial for assessing microbiota of skin. FIG. 5A shows settablematerial 510 applied to skin surface 500. Settable material includes aplurality of signal-generating complexes, each signal-generating complexincluding at least one signal-generating element 520 and at least onespecific microbe-binding element 530. In an aspect, the at least onesignal-generating element 520 is operably coupled to the at least onespecific microbe-binding element 530. FIG. 5B shows peelableskin-covering material 550 formed on skin surface 500 from settablematerial 510 in response to applied stimulus 540. Peelable skin-coveringmaterial 550 includes the plurality of signal-generating complexesincluding signal-generating element 520 and specific microbe-bindingelement 530. FIG. 5C shows peelable skin-covering material 550 with theplurality of signal-generating complexes including signal-generatingelement 520 and specific microbe-binding element 530.

FIG. 6 is a schematic cross-section through a peelable skin-coveringmaterial including a plurality of signal-generating complexes of a firsttype and a plurality of signal-generating complexes of a second type.FIG. 6A shows settable material 610 applied to skin surface 600.Settable material includes a plurality of signal-generating complexes ofa first type including signal-generating element of a first type 620 anda specific microbe-binding element of a first type 630 and a pluralityof signal-generating complexes of a second type includingsignal-generating element of a second type 640 and a specificmicrobe-binding element of a second type 650. In an aspect,signal-generating element of a first type 620 is operably coupled to aspecific microbe-binding element of a first type 630 andsignal-generating element of a second type 640 is operably coupled to aspecific microbe-binding element of a second type 650. Specificmicrobe-binding element of a first type 630 recognizes at least onefirst type of microbe while specific microbe-binding element of a secondtype 650 recognizes at least one second type of microbe.Signal-generating element 620 is configured to emit one or more signalsof a first type in response to the at least one first type of microbebound to operably coupled specific microbe-binding element 630 andsignal-generating element of a second type 640 is configured to emit oneor more signals of a second type in response to the at least one secondtype of microbe bound to operably coupled specific microbe-bindingelement of a second type 650. FIG. 6B shows peelable skin-coveringmaterial 670 formed on skin surface 600 from settable material 610 inresponse to applied stimulus 660. Peelable skin-covering material 670includes the plurality of signal-generating complexes of the first typeincluding signal-generating element of a first type 620 operably coupledto specific microbe-binding element of a first type 630 and theplurality of signal-generating complexes of the second type includingsignal-generating element of a second type 640 operably coupled tospecific microbe-binding element of a second type 650. FIG. 6C showspeelable skin-covering material 670 including the plurality ofsignal-generating complexes of the first type includingsignal-generating element of a first type 620 operably coupled tospecific microbe-binding element of a first type 630 and the pluralityof signal-generating complexes of the second type includingsignal-generating element of a second type 640 operably coupled tospecific microbe-binding element of a second type 650. In an aspect,peelable skin-covering material 670 is configured to detect at least twoor more types of microbes, each type of microbe binding to a specificmicrobe-binding element and eliciting a distinct and measureable signal,e.g., red versus green versus blue.

Specific Microbe-Binding Elements

In an aspect, each of the plurality of signal-generating complexesassociated with the skin-covering material includes at least onespecific microbe-binding element. The at least one specificmicrobe-binding element specifically recognizes at least one type ofmicrobe. The at least one type of microbe can include at least one typeof bacteria, fungus, virus, or parasite. In an aspect, the at least onespecific microbe-binding element recognizes at least one type ofmutualistic microbe, commensal microbe, or pathogenic microbe. In anaspect, the at least one specific microbe-binding element recognizes atleast one type of microbe resident on the skin surface of theindividual. Non-limiting examples of microbes have been described aboveherein.

In an aspect, the at least one specific microbe-binding element of thesignal-generating complex is configured to specifically recognize andbind a particular microbe or class of microbes. In an aspect, thespecific microbe-binding element may be specific for a particular typeof microbe, e.g., bacteria versus fungus. In an aspect, the specificmicrobe-binding element may be specific for Gram-positive versusGram-negative bacteria or a particular genus of microbes, e.g.,Propionibacterium versus Staphylococcus. In an aspect, the specificmicrobe-binding element may be specific for a particular species ofbacteria within a genus, e.g., S. aureus versus S. epidermidis.

Non-limiting examples of specific microbe-binding elements includeantibodies, aptamers, oligonucelotides, or anti-16S rRNAs. Othernon-limiting examples of specific microbe-binding elements includeantibody fragments, peptides, peptide nucleic acids, proteins, viruses,phospholipids, carbohydrates, enzymes, receptors, lectins, peptideaptamers, bacteria, cells, cell fragments, inorganic molecules, organicmolecules, artificial binding substrates (e.g., those formed bymolecular imprinting), or combinations thereof.

In an aspect, the specific microbe-binding element recognizes one ormore components of at least one type of microbe. In an aspect, thespecific microbe-binding element recognizes one or more biomoleculesassociated with the surface of a microbe, e.g., bacteria, a virus, afungus, or a parasite. In an aspect, the specific microbe-bindingelement recognizes components of microbe surface biomolecules includingamino acid sequences, oligosaccharides, proteoglycans, proteins,peptides, and/or lipids. For example, the specific microbe-bindingelement can recognize and bind teichoic acids and/or peptidoglycansassociated with Gram-positive bacteria. For example, the specificmicrobe-binding element can recognize and bind common lipopolysaccharidemoieties, e.g., 2-keto-3-deoxyoctanate, associated with Gram-negativebacteria. For example, the specific microbe-binding element canrecognize and bind chitin associated with fungi. In an aspect, thespecific microbe-binding element recognizes nucleic acids. For example,the specific microbe-binding element may be configured to recognize andbind one or more DNA or RNA sequence associated with the at least onetype of microbe.

In an aspect, the specific microbe-binding element recognizes one ormore biomolecules associated with the bacterial outer membrane, cellwall, and/or cytoplasmic membrane. Non-limiting examples of biomoleculesassociated with the bacterial outer membrane of Gram-negative bacteriainclude, but are not limited to, lipopolysaccaride and OMP (outermembrane protein) porins, the latter of which are exemplified by OmpC,OmpF and PhoP of E call Non-limiting examples of biomolecules associatedwith the bacterial cell wall of both Gram-positive and Gram-negativebacterial include, but are not limited to, peptidoglycans, i.e.,polymers composed of an alternating sequence of N-acetylglucoamine andN-acetyl-muraminic acid and crosslinked by amino acids and amino acidderivatives. Non-limiting examples of biomolecules associated with thebacterial cytoplasmic membrane include, but are not limited to, theMPA1-C (also called polysaccharide copolymerase, PCP2a) family ofproteins, the MPA2 family of proteins, and the ABC bacteriocin exporteraccessory protein (BEA) family of proteins. Other examples ofbiomolecules associated with bacteria include, but are not limited to,transporters, e.g., sugar porter (major facilitator superfamily),amino-acid/polyamine/organocation (APC) superfamily, cation diffusionfacilitator, resistance-nodulation-division type transporter, SecDF,calcium:cation antiporter, inorganic phosphate transporter, monovalentcation:proton antiporter-1, monovalent cation:proton antiporter-2,potassium transporter, nucleobase:cation symporter-2, formate-nitritetransporter, divalent anion:sodium symporter, ammonium transporter, andmulti-antimicrobial extrusion; channels, e.g., major intrinsic protein,chloride channel, and metal ion transporter; and primary activetransporters, e.g., P-type ATPase, arsenite-antimonite efflux, Type IIsecretory pathway (SecY), and sodium-transporting carboxylic aciddecarboxylase. A number of other potential biomolecules associated withbacteria have been described in Chung, et al. (2001) J. Bacteriology183:1012-1021, which is incorporated herein by reference.

In an aspect, the specific microbe-binding element recognizes one ormore biomolecules associated with at least one type of fungus.Non-limiting examples of biomolecules associated with fungi, e.g., theouter surface of fungi, include chitins and glucans, e.g., alpha glucans(dextran, glycogen, pullulan, starch) and beta glucans (cellulose,curdlan, laminarin, chrysolaninarin, lentinan, lichenin, pleuran,zymosan).

In an aspect, the specific microbe-binding element recognizes abiomolecule associated with at least one type of virus. For example, thespecific microbe-binding element may be configured to recognize and bindone or more capsid proteins of the virus. For example, the specificmicrobe-binding element may be configured to recognize and bind to VP5,a major capsid protein of herpes viruses.

In an aspect, the specific microbe-binding element can include aspecific microbe-binding antibody. For example, the specificmicrobe-binding antibody can include one or more antibodies configuredto recognize and bind one or more bacterium, fungus, and/or virus.Antibodies or fragments thereof for use in generating the specificmicrobe-binding element can include, but are not limited to, monoclonalantibodies, polyclonal antibodies, Fab fragments of monoclonalantibodies, Fab fragments of polyclonal antibodies, F(ab′)2 fragments ofmonoclonal antibodies, F(ab′)2 fragments of polyclonal antibodies,chimeric antibodies, non-human antibodies, fully human antibodies, amongothers. Single chain or multiple chain antigen-recognition sites can beused. Multiple chain antigen recognition sites can be fused or unfused.Antibody fragments can be produced by modification of whole antibodiesor synthesized de novo using recombinant DNA technologies. Antibodies orfragments thereof may be generated using standard methods.

Alternatively, an antibody or fragment thereof that recognizes at leastone type of microbe may be generated, for example, using phage displaytechnology. See, e.g., Kupper et al. (2005) BMC Biotechnology 5:4, whichis incorporated herein by reference. An antibody a fragment thereof, oran artificial antibody, e.g., Affibody® artificial antibodies (AffibodyAB, Bromma, Sweden) can be prepared using in silico design (Knappik etal. (2000) J. Mol. Biol. 296:57-86, which is incorporated herein byreference). In some embodiments, antibodies directed against specificmicrobes may be available from a commercial source (from e.g., NovusBiological, Littleton, Colo.; Sigma-Aldrich, St. Louis, Mo.; UnitedStates Biological, Swampscott, Mass.). Non-limiting sources ofantibodies designed to bind specific microbes, e.g., specific bacteria,fungi, viruses, or parasites, can be found in Linscott's Directory ofImmunological and Biological Reagents (accessible through the websiteaddress http://www.linscottsdirectory.com/).

In an aspect, the specific microbe-binding element includes a specificmicrobe-binding aptamer. The aptamer can be an oligonucleotide RNA- orDNA-based aptamer configured to recognize and bind one or more of abacteria, fungus, virus, or parasite. Aptamers are artificialoligonucleotides (DNA or RNA) that can bind to a wide variety ofentities (e.g., metal ions, small organic molecules, proteins, andcells) with high selectivity, specificity, and affinity. Aptamers may beisolated from a large library of 10¹⁴ to 10¹⁵ random oligonucleotidesequences using an iterative in vitro selection procedure termed“systemic evolution of ligands by exponential enrichment” (SELEX). See,e.g., Cao, et al (2005) Current Proteomics 2:31-40; Proske et al. (2005)Appl. Microbiol. Biotechnol. 69:367-374, which are incorporated hereinby reference. In general, SELEX may be used to generate aptamers againstany of a number of microbial targets, including but not limited tobacteria, fungi, viruses, and parasites. For example, Cao, et al.,describe using SELEX and whole bacteria to generate a panel of DNAaptamers configured to detect Staphylococcus aureus (in Nucleic AcidsRes., 37:4621-4628, 2009). See, e.g., Chen et al. (2007) Biochem.Biophys, Res. Commun. 357:743-748, Nitsche et al. (2007) BMC Biotechnol.7:48; Gopinath et al. (2012) J. Virol. 86:6732-6744; Low et al. (2009)Biochem. Biophys, Res. Commun. 386:544-548, which are incorporatedherein by reference.

In an aspect, the specific microbe-binding element includes apeptide-based aptamer, an artificial protein in which inserted peptidesare expressed as part of the primary sequence of a structurally stableprotein and having binding affinities comparable to antibodies. See,e.g., Crawford, et al., Brief Funct. Genomic Proteomic 2:72-79, 2003,which is incorporated herein by reference. Peptide aptamers can begenerated by screening a target, e.g., all or part of a microbe, againstyeast two-hybrid libraries, yeast expression libraries, bacterialexpression libraries and/or retroviral libraries.

In an aspect, the specific microbe-binding element includes a novelpeptide configured to specifically recognize and bind one or moremicrobes. Novel peptides that bind specific targets, e.g., a surfacecomponent of a bacteria, virus, or fungi, can be generated, for example,using phage display methodologies. See, e.g., Spear, et al. (2001)Cancer Gene Ther. 8:506-511, which is incorporated herein by reference.In an aspect, the phage express novel peptides on the surface as fusionproteins in association with a phage major or minor coat protein and canbe screened for binding interaction with one or more microbes.

In an aspect, the specific microbe-binding element can include a ligandthat specifically recognizes one or more microbes. For example, thespecific microbe-binding element can include CD14, which is associatedwith monocyte/macrophages and known to bind lipopolysaccharideassociated with Gram-negative bacteria as well as lipoteichoic acidassociated with the Gram-positive bacteria Bacillus subtilis (see, e.g.,Fan, et al. (1999) Infect. Immun. 67: 2964-2968). In an aspect, specificmicrobe-binding element can include all or part of a pattern recognitionreceptor that recognizes microbe-specific molecules (e.g., bacterialcarbohydrates, bacterial or viral DNA or RNA, bacterial peptides,peptidoglycans, lipoteichoic acids, N-formylmethionine, lipoproteins,and fungal glucans). Non-limiting examples of pattern recognitionreceptors with microbe-binding properties include toll-like receptors,C-type lectin receptors, NOD-like receptors, RIG-I-like receptors, RNAhelicases, complement receptors, collectins, ficolins, pentraxins,C-reactive proteins, lipid transferases, and the like. See, e.g., Modlin(2012) J. Invest. Dermatol. 132:882-886; Gauglitz et al. (2012) ActaDerm. Venereol. 92:291-298, which are incorporated herein by reference.

In an aspect, the specific microbe-binding element includes plasminogento bind a fungus, e.g., Candida albicans. See, e.g., Crowe et al. (2003)Mol. Microbiol. 47:1637-1651, which is incorporated herein by reference.

In an aspect, the specific microbe-binding element includes a lectin.Lectins include carbohydrate-binding proteins that bind cell surfaceglycoproteins and/or glycolipids. Because of the specificity that eachlectin has toward a particular carbohydrate structure, evenoligosaccharides with identical sugar compositions can be distinguishedor separated. Examples of lectins include, but are not limited to, algallectins, e.g., b-prism lectin; animal lectins, e.g., tachylectin-2,C-type lectins, C-type lectin-like, calnexin-calreticulin, capsidprotein, chitin-binding protein, ficolins, fucolectin, H-typelectins,I-type lectins, sialoadhesin, siglec-5, siglec-7, micronemal protein,P-type lectins, pentrxin, b-trefoil, galectins, congerins, selenocosmiahuwena lectin-I, Hcgp-39, Yml; bacterial lectins, e.g., PseudomonasPA-IL, Burkholderia lectins, chromobacterium CV-IIL, Pseudomonas PA IIL,Ralsonia RS-ILL, ADP-ribosylating toxin, Ralstonia lectin, Clostridiumhemagglutinin, botulinum toxin, tetanus toxin, cyanobacterial lectins,FimH, GafD, PapG, Staphylococcal enterotoxin B, toxin SSL11, toxin SSL5;fungal and yeast lectins, e.g., Aleuria aurantia lectin, integrin-likelectin, Agaricus lectin, Sclerotium lectin, Xerocomus lectin, Laetiporuslectin, Marasmius oreades agglutinin, agrocybe galectin, coprinusgalectin-2, Ig-like lectins, L-type lectins; plant lectins, e.g.,alpha-D-mannose-specific plant lectins, amaranthus antimicrobialpeptide, hevein, pokeweed lectin, Urtica dioica UD, wheat germ WGA-1,WGA-2, WGA-3, artocarpin, artocarpus hirsute AHL, banana lectin,Calsepa, heltuba, jacalin, Maclura pomifera MPA, MornigaM, Parkialectins, abrin-a, abrus agglutinin, amaranthin, castor bean ricin B,ebulin, mistletoe lectin, TKL-1, cyanovirin-N homolog, and variouslegume lectins; and viral lectins, e.g., capsid protein, coat protein,fiber knob, hemagglutinin, and tailspike protein. See, e.g., E. Bettler,R. Loris, A. Imberty “3D-Lectin database: A web site for images andstructural information on lectins” 3rd Electronic GlycoscienceConference, The internet and World Wide Web, 6-17 Oct. 1997;http://www.cermav.cnrs.fr/lectines/, which is incorporated herein byreference.

In an aspect, the specific microbe-binding element includes anartificial binding substrate formed by the process of molecularimprinting. In the process of molecular imprinting, a template, e.g., amicrobe or a surface component of a microbe, is combined with functionalmonomers which, upon cross-linking, form a polymer matrix that surroundsthe template. See, e.g., Alexander, et al. (2006) J. Mol. Recognit.19:106-180, which is incorporated herein by reference. Removal of thetemplate leaves a stable cavity in the polymer matrix that iscomplementary in size and shape to the template. In an aspect,functional monomers of acrylamide and ethylene glycol dimethacrylate canbe mixed with at least one type of microbe or parts thereof in thepresence of a photoinitiator and ultraviolet irradiation used tocross-link the monomers. The resulting polymer can be crushed or groundinto smaller pieces and washed to remove the at least one type ofmicrobe or parts thereof, leaving a particulate matrix material capableof binding the at least one type of microbe. Examples of otherfunctional monomers, cross-linkers and initiators that can be used togenerate an artificial binding substrate are provided. See, e.g., U.S.Pat. No. 7,319,038; Alexander, et al. (2006) J. Mol. Recognit.19:106-180, each of which is incorporated herein by reference. In anaspect, hydrogels can be used for molecular imprinting. Other examplesof synthetic binders are provided. See, e.g., U.S. Pat. Nos. 6,255,461;and 6,797,522; and Ye and Haupt (2004) Anal Bioanal Chem. 378:1887-1897; Peppas and Huang (2002) Pharm Res. 19: 578-587, each of whichis incorporated herein by reference.

In an aspect, the specific microbe-binding element recognizes and bindsDNA and/or RNA sequences associated with the at least one type ofmicrobe. In this instance, the one or more microbes may first besubjected to a lysis agent, e.g., a detergent, to make the cytoplasmiccomponents of the microbes more accessible. For example, the specificmicrobe-binding element may be a cDNA element engaged in DNA-DNAhybridization with microbe DNA sequence. In an aspect, the specificmicrobe-binding element may include oligonucleotides capable of bindingto unique 16S small subunit ribosomal (rRNA) genes. In an aspect,various phylogenetic markers may be targeted including ribosomal RNA,elongation and initiation factors, RNA polymerase subunits, DNA gyrases,heat shock proteins, and recA proteins.

In an aspect, the inner surface of the skin-covering material can bemodified with one or more materials that non-selectively interact withbiomolecules on the outer surface of microbes, e.g., proteins,polysaccharides, carbohydrates, phospholipids, proteoglycans, and thelike. In an aspect, the one or more materials take advantage of hydrogenbonding, electrostatic and/or hydrophobic interactions to capturemicrobes from the skin surface onto the inner surface of theskin-covering material. Non-limiting examples of materials includepoly-ionic surfaces, e.g., poly-cationic surfaces such as polyaminoacids (e.g., polylysine) and fibronectin for binding microbes that havean overall negative surface charge. Other non-limiting examples ofmaterials include nitrocellulose, cellulose nitrate, hydrophobicpolymers, PVDF coated surface, nylon coated surface, streptavidin coatedsubstrate to bind biotin labeled DNA, protein, peptide, Concanavalin A,and/or NETS-ester coated surface.

Signal-Generating Element

In an aspect, each of the plurality of signal-generating complexesassociated with the skin-covering material includes at least onesignal-generating element. In an aspect, the at least onesignal-generating element is operably coupled to at least one specificmicrobe-binding element, the at least one signal-generating elementconfigured to emit one or more signals in response to at least onemicrobe bound to the at least one operably coupled specificmicrobe-binding element. In an aspect, the signal-generating elementemits one or more signals in response to a structural change in thesignal-generating complex in the presence of a microbe. In an aspect,the signal-generating element emits one or more signals only when amicrobe is bound, e.g., an on/off detection system. Alternatively, thesignal-generating element emits a first signal type in the absence of abound microbe and a second signal type in the presence of a boundmicrobe, e.g., a change in the color or other property of emitted light.

In an aspect, the signal-generating complex can include at least onesignal-generating element configured to emit one or more signals inresponse to a chemical reaction, e.g., an enzymatic cleavage resultingin release of all or part of the signal-generating element, e.g., achromogenic or fluorogenic product. For example, the signal-generatingcomplex may include an enzymatically cleavable linkage to thesignal-generating element, the enzymatically cleavable linkage cleavedin response to an enzyme activity of a microbe.

Non-limiting examples of signal-generating elements include chromogenicsignal-generating elements, fluorogenic signal-generating elements,electrical signal-generating elements, radio signal-generating elements,electromagnetic signal-generating elements, acoustic signal-generatingelements, or magnetic signal-generating elements. In an aspect, the atleast one signal-generating element can emit one or more of achromogenic signal, a fluorescent signal, an electromagnetic signal, anacoustic signal, or a luminescent signal. Non-limiting examples ofsignal-generating elements include, but are not limited to, at least oneof a chromogenic element, a fluorogenic element, a quantum dot, a dye,or chemiluminescent dye, or a combination thereof. Other non-limitingexamples of signal-generating elements include a radioactive element; aradiopaque dye; a radiofrequency identification tag; a contrast agent, avisible dye, volatile label; mass label; luminescent label, e.g.,bioluminescent or chemiluminescent; metallic label, e.g., goldparticles, magnetic beads, or paramagnetic beads; dyes, e.g., direct,indirect, or releasable; or a combination thereof.

In an aspect, the signal-generating element is a chromogenic orfluorogenic signal-generating element. In an aspect, the chromogenic orfluorogenic signal-generating element can be a chemical entity operablycoupled to the specific microbe-binding element that changes color inresponse to an interaction with a microbe, e.g., binding the microbe. Inan aspect, the chromogenic or fluorogenic signal-generating element canchange color in response to metabolism of a microbe bound to and/or inproximity to the inner surface of the skin-covering material. In anaspect, the chromogenic or fluorogenic signal-generating element canchange color in response to one or more components excreted from amicrobe in proximity to the signal-generating complex. For example, thechromogenic or fluorogenic signal-generating element can by linked tometabolic activity of certain classes of biochemicals including sugars,hexo-phoshates, amino acids, hexose sugars, carboxylic acids, esters,and fatty acids. In an aspect, the chromogenic or fluorogenicsignal-generating element can change color in response to an interactionwith a microbe independent of the specific microbe-binding element. Forexample, the chromogenic or fluorogenic signal-generating element caninclude tetrazolium salts which form violet-colored formazans inresponse to microbe metabolism. See, e.g., Tachon et al. (2009)Microbiology 155:2941-2948, which is incorporated herein by reference.

In an aspect, the signal-generating complex can include asignal-generating element that is a chromogenic substrate. Chromogenicsubstrates can include peptides that generate color in response tointeraction with microbe-derived proteolytic enzymes. For example, thechromogenic substrate may include in part a chemical group, e.g.,para-nitroaniline, which generates a color change when released byenzymatic cleavage. For example, a chromogenic substrate associated withthe skin-covering material may interact with an enzyme located on theexterior of the microbe, e.g., located in a bacterial cell wall, togenerate a color signal. As an example, L-alanine-4-nitroanilide can beused as a chromogenic substrate for L-alanine-aminopeptidase, commonlyassociated with Gram-negative bacteria. The substrateL-alanine-4-nitroanilide is split by L-alanine aminopeptidases intoL-alanine and 4-nitroaniline, the latter producing a yellow color. Thecolor change can be followed spectrophotometrically and may beproportional to the proteolytic activity.

In an aspect, the signal-generating complex can include asignal-generating element that is a fluorogenic signal-generatingelement. In an aspect, fluorogenic signal-generating elements caninclude chemical dyes or fluorophores that emit light, i.e., fluoresce,at various wavelengths in response to excitation energy. In an aspect,the fluorogenic signal-generating element can include a quantum dot orsemiconductor nanocrystals that fluoresce at various wavelengths inresponse to excitation energy. See, e.g., Jaiswal et al. (2003) NatureBiotech. 21:47-51, which is incorporated herein by reference.Non-limiting examples of fluorophores for use as fluorogenicsignal-generating elements include fluorescein (FITC), indocyanine green(ICG) and rhodamine B, red and near infrared emitting fluorophores(600-1200 nm) including cyanine dyes such as Cy5, Cy5.5, and Cy7(Amersham Biosciences, Piscataway, N.J., USA) and/or a variety of AlexaFluor dyes such as Alexa Fluor 633, Alexa Fluor 635, Alexa Fluor 647,Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 700 and Alexa Fluor 750(Molecular Probes-Invitrogen, Carlsbad, Calif., USA). Additionalfluorophores include IRDye800, IRDye700, and IRDye680 (LI-COR, Lincoln,Nebr., USA), NIR-1 and 1C5-OSu (Dejindo, Kumamotot, Japan), LaJolla Blue(Diatron, Miami, Fla., USA), FAR-Blue, FAR-Green One, and FAR-Green Two(Innosense, Giacosa, Italy), ADS 790-NS and ADS 821-NS (American DyeSource, Montreal, Calif.), NIAD-4 (ICx Technologies, Arlington, Va.).Other fluorescing dyes include BODIPY-FL, europium, green, yellow andred fluorescent proteins, luciferase.

In an aspect, the signal-generating complex includes a signal-generatingelement that is a magnetic signal-generating element, e.g., magneticbeads or particles. In an aspect, the signal-generating complex caninclude magnetic beads or particles conjugated to the complex via anenzymatically cleavable linkage which in the presence of a microbe iscleaved, releasing the magnetic bead or particle. In an aspect, Magneticbeads and magnetic particles of various sub-millimeter size areavailable from commercial sources (e.g., from Seradyn-Thermo Scientific,Indianapolis, Ind.; Dynal-Invitrogen, Carlsbad, Calif.).

In an aspect, the signal-generating complex includes a signal-generatingelement that is a radiofrequency identification tag. In an aspect, thesignal-generating complex can include a radiofrequency identificationtag conjugated to the complex via an enzymatically cleavable linkagewhich in the presence of a microbe is cleaved, releasing theradiofrequency identification tag. In an aspect, the signal-generatingelement can include a sub-millimeter radiofrequency identification tag.See, e.g., Hornyak (2008) Scientific American Magazine, pp 68-71,February 2008, which is incorporated herein by reference. Alternatively,the signal-generating element can include one or more bokodes,millimeter sized visual tags that can be captured with a camera. See,e.g., Mohan et al. ACM Transactions on Graphics Proceedings of SIGGRAPH2009, Aug. 3-7, 2009, New Orleans, which is incorporated herein byreference.

In an aspect, the signal-generating complex can be configured such thatbinding of one or more microbes to the specific microbe-binding elementoperably coupled to the signal-generating element results in aconformational change that can be measured using fluorescence resonanceenergy transfer (FRET). FRET is a distance-dependent interaction betweenthe electronic excited states of two dye molecules in which excitationis transferred from a donor molecule to an acceptor molecule withoutemission of a photon. In an aspect, interaction of a donor molecule withan acceptor molecule can lead to a shift in the emission wavelengthassociated with excitation of the acceptor molecule. In an aspect,interaction of a donor molecule with an acceptor molecule can lead toquenching of the donor emission. In an aspect, the signal-generatingcomplex can include at least one signal-generating element that includesat least one donor molecule and at least one acceptor molecule attachedto a specific microbe-binding element, e.g., an antibody or aptamer. Inthis configuration, interaction of at least one type of microbe with thespecific microbe-binding element, e.g., the antibody or aptamer, causesa conformational change in the specific microbe-binding element andresults in a change in the distance between the donor and acceptormolecules components of the signal-generating element and a change inmeasurable signal, e.g., fluorescence.

A variety of donor and acceptor fluorophore pairs can be considered forFRET including, but not limited to, fluorescein andtetramethylrhodamine; IAEDANS and fluorescein; fluorescein andfluorescein; and BODIPY FL and BODIPY FL. A number of Alexa Fluor (AF)fluorophores (Molecular Probes-Invitrogen, Carlsbad, Calif., USA) can bepaired with other AF fluorophores for use in FRET. Some examplesinclude, but are not limited, to AF 350 with AF 488; AF 488 with AF 546,AF 555, AF 568, or AF 647; AF 546 with AF 568, AF 594, or AF 647; AF 555with AF594 or AF647; AF 568 with AF6456; and AF594 with AF 647.

Other non-limiting examples of fluorophores for FRET-based signalinginclude cyanine dyes Cy3, Cy5, Cy5.5 and Cy7, which emit in the red andfar red wavelength range (>550 nm). For example, Cy3, which emitsmaximally at 570 nm and Cy5, which emits at 670 nm, can be used as adonor-acceptor pair. When Cy3 and Cy5 are not proximal to one another,excitation at 540 nm results only in the emission from of light from Cy3at 590 nm. In contrast, when Cy3 and Cy5 are brought into proximity by aconformation change, e.g., by binding of a microbe to a specificmicrobe-binding element, excitation at 540 nm results in an emission at680 nm.

In an aspect, the signal-generating element includes a quenching dye toquench the fluorescence of visible light-excited fluorophores.Non-limiting examples of quenching dyes include DABCYL, thenon-fluorescing diarylrhodamine derivative dyes QSY 7, QSY 9 and QSY 21(Molecular Probes, Carlsbad, Calif., USA), the non-fluorescing BlackHole Quenchers BHQO, BHQ1, BHQ2, and BHQ3 (Biosearch Technologies, Inc.,Novato, Calif., USA) and Eclipse (Applera Corp., Norwalk, Conn., USA).Non-limiting examples of donor fluorophore and quencher pairs includefluorescein with DABCYL; EDANS with DABCYL; or fluorescein with QSY 7and QSY 9. In general, QSY 7 and QSY 9 dyes efficiently quench thefluorescence emission of donor dyes including blue-fluorescentcoumarins, green- or orange-fluorescent dyes, and conjugates of theTexas Red and Alexa Fluor 594 dyes. QSY 21 dye efficiently quenches allred-fluorescent dyes. A number of the Alexa Fluor (AF) fluorophores(Molecular Probes-Invitrogen, Carlsbad, Calif., USA) can be paired withquenching molecules as follows: AF 350 with QSY 35 or DABCYL; AF 488with QSY 35, DABCYL, QSY7 or QSY9; AF 546 with QSY 35, DABCYL, QSY7 orQSY9; AF 555 with QSY7 or QSY9; AF 568 with QSY7, QSY9 or QSY21; AF 594with QSY21; and AF 647 with QSY 21.

In an aspect, the signal-generating complex for FRET-based signalingincludes a specific microbe-binding element that is an RNA or DNAoligonucleotide-based aptamer and a signal-generating element thatincludes one or more donor fluorophore and one or more acceptorfluorophore or quencher. See, e.g., Cao et al. (2005) Current Proteomics2:31-40 and U.S. Patent Application 2009/0186342, which are incorporatedherein by reference. For example, the aptamer including a donorfluorophore and an acceptor fluorophore or quencher can be configured toundergo a conformational change upon binding a target, e.g., a microbe,causing the distance between the donor fluorophore and the acceptorfluorophore or quencher to shift and leading to a change in measurablefluorescence. See, e.g., Ikanovic et al. (2007) J. Fluorescence17:193-199, which is incorporated herein by reference. As describedabove herein, aptamers against a variety of targets, including wholemicrobes, can be isolated from a large library of 10¹⁴ to 10¹⁵ randomoligonucleotide sequences using an iterative in vitro selectionprocedure often termed “systematic evolution of ligands by exponentialenrichment” (SELEX).

In an aspect, an aptamer-based signal-generating complex includes atleast one signal-generating element that is a semiconductor quantum dot(QDs). Various methods are available for attaching quantum dots to theDNA backbone of an aptamer such as, for example, covalent linkage ofamine-modified DNA to carboxylated quantum dots and linkage ofbiotinylated DNA to streptavidin modified quantum dots. See, e.g., Cady,et al. (2007) J. Mol. Cell. Probes 21:116-124, which is incorporatedherein by reference. For example, carboxy quantum dots (from, e.g.,Quantum Dot Corporation, Hayward, Calif., USA) can be attached to anaptamer through a C6 amino modifier placed on either the 5-prime or3-prime end of the aptamer sequence. For example, streptavidin quantumdots (from, e.g., Quantum Dot Corporation, Hayward, Calif., USA) can beattached to an aptamer through a biotin attached to the 5-prime end ofthe aptamer sequence.

In an aspect, the aptamer-based signal-generating complex includes asignal-generating element that is a fluorophore, non-limiting examplesof which have been describe above herein. The fluorophores can beattached to various linkers that allow for attachment at various siteswithin the aptamer. For example, 3-prime-DABCYL CPG can be used to placethe fluorophore DABCYL at the 3-prime terminus of the aptamer whereas5-prime-DABCYL phosphoramidite can be used to place DABCYL at the5-prime terminus of the aptamer (see, e.g., product information at GlenResearch, Sterling, Va.). DABCYL deoxythymidine (dT) can be used toplace DABCYL within the body of the aptamer sequence. Modifying aptamerswith appropriate commercially available fluorophores can be achievedfollowing instructions provided by the respective manufacturer.Alternatively, custom made aptamer-based signaling complexes areavailable from commercial sources (from, e.g., Biosearch Technologies,Inc., Novato, Calif., USA).

In an aspect, the aptamer-based signal-generating complex can have asignal-generating element in a region of the molecule known to undergoconformational change upon binding a target microbe that leads to anincrease in fluorescence intensity. An aptamer of this sort can beselected using an in vitro selection process with fluorescently labeledaptamers. See, e.g., Jhaveri, et al. (2000) Nature Biotech.18:1293-1297, which is incorporated herein by reference. For example, apool of RNA molecules is generated in which the random sequence region(45-60 residues) is skewed such that one of the residues, uridine, forexample, is disproportionately underrepresented. The three to fourrandomly placed uridine residues are substituted withfluorescein-12-UTP, Cascade Blue-7-UTP, Texas Red-5-UTP, and/orRhodamine Green-5-UTP during in vitro transcription. The labeled pool ofRNA molecules are screened against a target microbe by passing thelabeled pool over a column matrix or other matrix to which the targetmicrobe is attached. Those RNA molecules that bind with high affinity tothe target component are screened for their fluorescence signalingproperties in response to binding of the target microbe. For example,the baseline fluorescence intensity is measured for RNA aptamermolecules labeled with fluorescein-12-UTP (excitation maxima 494 nm,emission maxima 521 nm) or Rhodamine Green-5-UTP (excitation maxima 505nm, emission maxima 533 nm), for example, then re-measured in responseto increasing concentrations of the target component. As such,fluorescent aptamers can be selected that exhibit a 100-200% increase influorescence intensity in response to target binding.

In an aspect, the signal-generating complex for FRET-based signalingincludes a specific microbe-binding element that is an antibodyconfigured to bind at least one type of microbe and a signal-generatingelement that includes one or more donor fluorophore and one or moreacceptor fluorophore or quencher. For example, the antibody including adonor fluorophore and an acceptor fluorophore or quencher can beconfigured to undergo a conformational change upon binding a target,e.g., a microbe, causing the distance between the donor fluorophore andthe acceptor fluorophore or quencher to shift, the shift leading to achange in measurable fluorescence. See, e.g., Dwarakanath et al. (2004)Biochem. Biophys. Res. Commun. 323:739-743, which is incorporated hereinby reference. In an aspect, the antibody can be designed to elicit ashift in emission wavelength, for example, in response to binding amicrobe. For example, an antibody exhibiting a shift in fluorescentsignal in response to binding of a target microbe can be generated bylabeling the antibody with a solvent-sensitive fluorophore, e.g., dansylchloride (5-dimethylaminonaphthalene-1-sulfonyl chloride). See, e.g.,Brennan (1999) J. Fluor. 9:295-312, which is incorporated herein byreference. In an aspect, the antibody is modified with a fluorescencesignal-generating element such that binding of the target microbe to theantibody shields a solvent sensitive fluorescence signal-generatingelement near the active binding site from a solvent, e.g., water,resulting in a 3-5 fold increase in fluorescence intensity. See, e.g.,Bright, et al. (1990) Anal. Chem. 62:1065-1069, which is incorporatedherein by reference.

In an aspect, the signal-generating complex for FRET-based signalingincludes a specific microbe-binding element that is an antibody with aflexible arm. For example, the antibody can include a donor fluorophorenear the binding site of a target, e.g., a microbe, as well as aflexible arm containing an analog of the target or part thereof that islabeled with a quencher and recognized by the antibody. See, e.g. U.S.Patent Application 2006/0172318, which is incorporated herein byreference. For example, as the labeled target analog moves intoproximity to the labeled active site, a baseline FRET signal can bemeasured. A measurable change in the FRET signal is detected when theanalog is competitively displaced by the actual target. The flexible armcan be composed of DNA, RNA, polymers, protein nucleic acid (PNA),peptides, protein or oligosaccharide. For example, anamino-functionalized DNA arm can be treated with a bifunctionalNETS-ester activated Cy3.5 dye to add a fluorescent tag to the flexiblearm. The analog of the target is modified with a monoamine andinteracted with the bifunctional NETS-ester and attached to the DNAflexible arm. The flexible arm can be attached directly to the antibodythrough a thiol-maleimide linkage such that the DNA flexible arm ismodified with a thiol group at one end and linked via maleimide to oneor more cysteine groups on the antibody. Alternatively, the flexible armcan be attached to a protein, for example, that is adjacent to theantibody or to which the antibody is bound.

In an aspect, the signal-generating complex can be configured such thatbinding of one or more microbes to the specific microbe-binding elementoperably coupled to the signal-generating element results in aconformational change that can be measured using chemiluminescenceresonance energy transfer (CRET). In an aspect, the image-capture deviceis able to detect luminescence. For example, the interaction of luminolwith hydrogen peroxide in the presence of iron or copper and enhanced byhorseradish peroxidase results in emitted light. See, e.g., Freeman etal. (2011) J. Am. Chem. Soc. 133:11597-11604; Lee et al. (2012) ACS Nano6:2978-2983, which are incorporated herein by reference.

In an aspect, the at least one specific microbe-binding element of thesignal-generating complex is chemically coupled to the at least onesignal-generating element. In an aspect, the specific microbe-bindingelement and the signal-generating element are directly associated withone another through chemical cross-linking, non-covalent linking, orsynthesis as a single molecule. For example, the signal-generatingelement may be operably coupled to the specific microbe-binding elementthrough one or more of a chemical cross-link, a streptavidin/biotininteraction, a fusion protein construct, a common substrate, or acombination thereof.

In an aspect, the signal-generating element is conjugated to thespecific microbe-binding element using one or more of a cross-linkingagent, non-limiting examples of which have been describe above herein.In general, any of a number of cross-linking agents can be used toconjugate an appropriately derivatized signal-generating element to anappropriately derivatized or functionalized specific microbe-bindingelement. For example, a fluorescent dye, e.g., rhodamine, derivatizedwith succinimidyl ester (from, e.g., Invitrogen, Carlsbad, Calif.) willreact efficiently with primary amines of proteins, e.g., antibodies, togenerate a stable fluorescent dye-protein conjugate. As another example,an antibody for use as a specific microbe-binding element can beconjugated with one or more quantum dots via an amine-thiol linkageusing amine-derivatized, poly-ethylene glycol coated quantum dots andthe amine-thiol crosslinker SMCC using a commercially available kit(Qdot® Antibody Conjugation Kit, Invitrogen, Carlsbad, Calif.).Similarly, various methods are available for attaching quantum dots to aDNA backbone of an aptamer such as, for example, covalent linkage ofamine-modified DNA to carboxylated quantum dots. For example, carboxyquantum dots (from, e.g., Quantum Dot Corporation, Hayward, Calif., USA)can be attached to an aptamer through a C6 amino modifier placed oneither the 5-prime or 3-prime end of the aptamer sequence. Magneticbeads derivatized with carboxylic acid, amine groups or tosylactivatedfor cross-linking to proteins and appropriately derivatizedoligonucleotides are also commercially available (from, e.g., DynalBiotech, Brown Deer, Wis.). Quantum dots, fluorescent dyes, and magneticparticles derivatized for cross-linking to antibodies, aptamers or otherbiomolecules are available from a number of commercial sources (from,e.g., Invitrogen, Carlsbad, Calif.; Seradyn-Thermo Scientific,Indianapolis, Ind.; Sigma-Aldrich, St. Louis, Mo.). Non-limitingexamples of homobifunctional, heterobifunctional, and/or photoreactivecross-linking agents have been described above herein.

In an aspect, the at least one specific microbe-binding element isnon-covalently lined to the signal-generating element. For example, thesignal-generating element can be non-covalently linked to the specificmicrobe-binding element using one or more interactions between biotinand avidin, streptavidin or derivatives thereof. In an aspect, abiotinylated signal-generating element can be reacted with abiotinylated specific microbe-binding element in the presence ofstreptavidin to form the signal-generating complex. For example, abiotinylated signal-generating element, e.g., biotin-4-fluorescein(from, e.g., Invitrogen, Carlsbad, Calif.), can be linked to abiotinylated specific microbe-binding element, e.g., a biotinylatedantibody, through a streptavidin bridge. An antibody or otherprotein-based binding component can be biotinylated using an aminereactive biotinylation reagent such as, for example, EZ-LinkSulfo-NHS—SS-Biotin (sulfosuccinimidyl 2-(biotinamido)-ethyl-1,3-dithiopropionate; Pierce-Thermo Scientific, Rockford, Ill., USA; see,e.g., Jaiswal, et al. Nature Biotech. 21:47-51, 2003, which isincorporated herein by reference). Similarly, a biotinylated label canbe linked to a biotinylated oligonucleotide aptamer through astreptavidin bridge. An aptamer or other nucleotide-based bindingcomponent can be biotinylated by introducing a biotinylated nucleotide,e.g., biotin-5-deoxycytidine-5-triphosphate (from, e.g., ChemCyte, Inc.,San Diego, Calif.) into the aptamer sequence during in vitrotranscription.

In an aspect, the signal-generating element or the specificmicrobe-binding element of can be modified with streptavidin, avidin, orderivative thereof and directly bound to a biotinylatedsignal-generating element or a specific microbe-binding element. In anaspect, the signal-generating element is modified with streptavidin andcombined with a biotinylated specific microbe-binding element. Forexample, streptavidin modified quantum dots (available from, e.g.,Quantum Dot Corporation, Hayward, Calif., USA) can be attached to anaptamer through a biotin modification to the 5-prime end of the aptamersequence. See, e.g., Cady et al. (2007) Mol. Cell. Probes 21:116-124,which is incorporated herein by reference. Examples of otherstreptavidin modified fluorescent dyes are available (from, e.g.,PerkinElmer, Waltham, Mass.; Alpha Diagnostic Intl. Inc., San Antonio,Tex.). Streptavidin modified magnetic beads are also commerciallyavailable (e.g., Dynabeads® MyOne™ Streptavidin, Dynal Biotech, BrownDeer, Wis.). In another aspect, the specific microbe-binding element cancontain all or part of the streptavidin protein for use in binding to abiotin modified signal-generating element. For example, cDNA sequenceencoding all or part of an antibody or other protein/peptide can begenetically modified to contain all or part of the streptavidin geneusing standard cloning procedures, resulting in a streptavidin-antibodyfusion protein. See, e.g., Koo, et al. (1998) Appl. Environ. Microbiol.64:2497-2502, which is incorporated herein by reference. Thestreptavidin modified specific microbe-binding element can subsequentlybe combined with one or more of a biotinylated signal-generatingelement.

In an aspect, the signal-generating element can be incorporated into thespecific microbe-binding element at the time of synthesis. In an aspect,the signal-generating complex can include a fusion protein with aspecific microbe-binding element, e.g., antibody, peptide ligand, orreceptor, and a signal-generating element including all or part of greenfluorescent protein (GFP) derived from Aequorea victoria jellyfish oryellow, red and blue fluorescing derivatives thereof. A number ofexpression constructs for generating recombinant GFP fusion proteins areavailable from commercial sources (from, e.g., Invitrogen, Carlsbad,Calif.).

In an aspect, the plurality of signal-generating complexes associatedwith the inner surface of the skin-covering material are incorporatedinto a field effect transistor (FET) based biosensor, in which a changein electrical signal is used to detect interaction of one or moremicrobes with one or more of the plurality of signal-generatingcomplexes. See, e.g., U.S. Pat. No. 7,303,875, which is incorporatedherein by reference. In an aspect, the one or more electrical signalsare processed to generate one or more optical signals usinglight-emitting diodes or semiconductor optical amplifier, the one ormore optical signals detected by the image-capture device. In an aspect,the signal-generating complex can include carbon nanotubesfunctionalized with a specific microbe-binding element. See, e.g.,Zelada-Guillen, et al., (2009) Angew. Chem. Int. Ed., 48:7334-7337,which is incorporated herein by reference. Single walled carbonnanotubes can act as efficient ion-to-electron transducers inpotentiometric analysis. The carbon nanotubes can be functionalized witha specific microbe-binding element, e.g., an oligonucleotide aptamer,configured recognize and bind at least one type of microbe. The specificmicrobe-binging element is modified with an amine group and covalentlyimmobilized onto a layer of previously carboxylated single-walled carbonnanotubes. The aptamers are self-assembled on the carbon nanotubesthrough stacking interactions between the purine and pyrimidine bases ofthe oligonucleotide aptamers and the walls of the carbon nanotubes. Uponmicrobe binding to the aptamer, the aptamers change conformation,separating the phosphate groups of the aptamer from the side-walls ofthe carbon nanotubes and inducing a charge change to the carbon nanotubeand recorded potential.

In an aspect, the signal-generating complex can include one or moremicrocantilevers configured to detect changes in cantilever bending orvibrational frequency in response to binding of one or more microbes tothe surface of the microcantilever. In an aspect, the inner surface ofthe skin-covering material can include a plurality of biochips includingmicrocantilever bi-material formed from gold and silicon, as sensingelements. See, e.g. Vashist (2007) J. Nanotech Online 3:DO:10.2240/azojono0115, which is incorporated herein by reference. The goldcomponent of the microcantilever can be functionalized with one or morespecific microbe-binding elements, e.g., aptamer, antibodies, or othermicrobe binding element. A number of microcantilever deflectiondetection methods can be used to measure microbe binding including,among other things, optical deflection detection, interferometrydeflection detection, optical diffraction grating deflection detection,and charge coupled device detection. In some aspects, the one or moremicrocantilever can be a nanocantilever with nanoscale components. Theone or more microcantilevers and/or nanocantilevers can be arranged intoarrays for detection of one or more target cells. Both microcantileversand nanocantilevers can find utility in microelectromechnical systems(MEMS) and/or nanoelectromechnical systems (NEMS).

In an aspect, the signal-generating complex can include one or moresurface plasmon resonance sensors for detecting changes in therefractive index on a sensor surface in response to changes in moleculesbound on the sensor surface. In an aspect, the inner surface of theskin-covering material is coated with a thin film of metal, for example,gold. In an aspect, the surface includes a matrix to which isimmobilized a plurality of specific microbe-binding elements. The sensoris illuminated by monochromatic light. Resonance occurs at a specificangle of incident light. The resonance angle depends on the refractiveindex in the vicinity of the surface, which is dependent upon theconcentration of microbes on the surface. See, e.g., Raghavan & Bjorkman(1995) Structure 3:331-333, which is incorporated herein by reference.

In an aspect, the skin-covering material is reusable. In an aspect, theplurality of signal-generating complexes including at least onesignal-generating element operably coupled to at least one specificmicrobe-binding element are included in a renewable layer on the innersurface of the skin-covering material. For example, the plurality ofsignal-generating complexes including at least one signal-generatingelement operably coupled to at least one specific microbe-bindingelement may be applied to the inner surface of the skin-coveringmaterial as a liquid, gel, or spray, rinsed off the skin-coveringmaterial after a first use, and reapplied for subsequent uses. In anaspect, at least one of the signal-generating element, the specificmicrobe-binding element, or both are renewable. For example, a change inpH, ionic strength, temperature, or combinations thereof may be used tonon-destructively remove microbes bound to the specific microbe-bindingelement. In this way, a single skin-covering material can be preparedfor an individual and used multiple times with regenerated or replacedsignal-generating complexes.

Systems Including Skin-Covering Material

FIG. 7 illustrates aspects of a system for assessing the microbiota ofskin including a skin-covering material. System 700 includes componentsconfigured to sample and report to a user the identity and the spatialdistribution of microbes contributing to the microbiota on a skinsurface of an individual. System 700 includes skin-covering material710, an image-capture device 720, and a computing device 730.

Skin-covering material 710 includes an inner surface and an outersurface, the inner surface substantially conforming in shape to atopography of a skin surface of individual 740. In an aspect,skin-covering material 710 is configured to be in physical contact withthe skin surface of individual 740 and to interact, e.g., bind, at leastone type of microbe from the skin surface of individual 740.

The inner surface of skin-covering material 710 further includes aplurality of signal-generating complexes, one or more of the pluralityof signal-generating complexes configured to emit one or more signals inresponse to at least one type of microbe. In an aspect, skin-coveringmaterial 710 can include a pre-formed skin-covering material, e.g., asillustrated in FIG. 1. Non-limiting aspects of a pre-formedskin-covering have been described above herein. In an aspect,skin-covering material 710 can include a peelable skin-coveringmaterial, e.g., as illustrated in FIG. 2. Non-limiting aspects of apeelable skin-covering material have been described above herein. In anaspect, skin-covering material 710 can include a plurality ofsignal-generating complexes, each of the signal-generating complexesincluding at least one signal-generating element operably coupled to atleast one specific microbe-binding element, e.g., as illustrated in FIG.3 and in FIG. 5.

In an aspect, skin-covering material 710 includes a plurality ofsignal-generating complexes of at least one first type including atleast one signal-generating element of a first type operably coupled toat least one specific microbe-binding element of a first type, the atleast one signal-generating element of the first type configured to emitone or more signals of a first type in response to at least one firsttype of microbe bound to the operably coupled at least one specificmicrobe-binding element of the first type and a plurality ofsignal-generating complexes of at least one second type including atleast one signal-generating element of a second type operably coupled toat least one specific microbe-binding element of a second type, the atleast one signal-generating element of the second type configured toemit one or more signals for a second type in response to at least onesecond type of microbe bound to the operably coupled at least onespecific microbe-binding element of the second type, e.g., asillustrated in FIG. 4 and FIG. 6. In an aspect, the at least one firsttype of microbe differs from the at least one second type of microbe. Inan aspect, the one or more signals of the first type differ from the oneor more signals of the second type.

System 700 includes image-capture device 720. Image-capture device 720includes circuitry to capture at least one image of the inner surface ofskin-covering material 710, the at least one image including one or moresignals emitted from one or more of the plurality of signal-generatingcomplexes and to transform the captured at least one image into adigital output including information associated with at least oneproperty and a spatial distribution of the imaged one or more signals.In an aspect, image-capture device 720 includes an energy emittingmechanism that emits directed energy 750, excitation energy, whichelicits one or more signals 760, e.g., emission energy, from one or moreof the plurality of signal-generating complexes associated withskin-covering material 710. In an aspect, image-capture device 720includes at least one camera. In an aspect, image-capture device 720includes at least one scanning device. The at least one scanning devicecan include at least one of a passive scanning device, an activescanning device, or a three-dimensional scanning device. Othernon-limiting examples of scanning devices include at least one of anoptical scanning device, a fluorescence scanning device, an acousticscanning device, an electromagnetic scanning device, a spectrometer, ora spectrophotometer.

System 700 further includes computing device 730. Computing device 730includes a processor and is operably coupled to image-capture device 720through a communication link 715. Communication link 715 can include atleast one of a wireless communication link, e.g., Bluetooth or otherradio transmission link, or a wired communication link, e.g., anelectrical link. Computing device 730 includes circuitry configured toreceive the digital output from image-capture device 720 including theinformation associated with the at least one property and the spatialdistribution of the imaged one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to theat least one microbe, compare the properties of the imaged one or moresignals emitted from the one or more of the plurality ofsignal-generating complexes with a database of emitted signals ofreference signal-generating complexes, and generate digital spatialprofile 770 of the at least one type of microbe based on the spatialdistribution of the imaged one or more signals emitted from the one ormore of the plurality of signal-generating complexes. In an aspect,computing device 730 further includes circuitry to generate a digitalalignment 780 of digital spatial profile 770 with a digital image of askin surface of individual 740. Digital alignment 780 can be reported toa user of the system, e.g., individual 740 or another individual, to aidin determining a recommended treatment regimen to maintain or alter thecurrent types and spatial distribution of microbes on the skin surfaceof the individual.

Image-Capture Device

Returning to FIG. 7, system 700 for assessing the microbiota of the skinsurface of an individual includes image-capture device 720 includingcircuitry configured to capture at least one image of the inner surfaceof skin-covering material 710. In an aspect, image-capture device 720includes an energy-emitting mechanism and circuitry to scan the innersurface of skin-covering material 710 with directed energy 750 to detectone or more signals 760 emitted from the inner surface of skin-covering710 and to transform the one or more detected signals into a digitaloutput for receipt by computing device 730. The digital output includesinformation associated with at least one property and a spatialdistribution of the detected one or more signals emitted from the one ormore of the plurality of signal-generating complexes.

In an aspect, the at least one property of the one or more signalsemitted from the one or more of the plurality of signal-generatingcomplexes in response to the at least one type of microbe includes atleast one optical property, fluorescence property, acoustic property,electrical property, magnetic property, or electromagnetic property. Inan aspect, the at least one property of the one or more signals emittedfrom the at least one of the plurality of the at least one type ofsignal-generating element includes at least one of wavelength,frequency, or amplitude. The one or more signals generated by theplurality of the at least one type of signal-generating element can bedetected by image-capture device 720 using any of a number of imaging oroptical methods including but not limited to light scattering,electrical impedance, infrared spectroscopy, acoustic imaging, thermalimaging, photothermal imaging, dark field, visible light absorption andrefraction, and autofluorescence. In an aspect, the image-capture devicemeasures the absorption, emission, fluorescence, luminescence,chemiluminescence, and/or phosphorescence of the one or moresignal-generating complexes. See, e.g., Doornbos et al. (1993) Cytometry14:589-594; Gao et al. Proceedings of the 25^(th) Annual InternationalConference of the IEEE EMBS, Cancun, Mexico, Sep. 17-21, 2003;Oberreuter et al. (2002) Int. J. Syst. Evol. Microbiol. 52:91-100;Baddour et al. (2002) Ultrasonics Symposium IEEE 2:1639-1644; Zharov etal. (2006) J. Cell. Biochem. 97:916-932; Zharov et al. (2006) J. Biomed.Opt. 11:054034-1-4; Koenig et al. (1994) J. Fluoresc. 4:17-40; each ofwhich is incorporated herein by reference.

In an aspect, image-capture device 720 includes at least one camera,e.g., a digital camera, configured to capture one or more images. In anaspect, the at least one camera may capture one or more images in thevisible spectrum. In an aspect, the at least one camera may capture oneor more images in other portions of the electromagnetic spectrum, e.g.,infrared or ultraviolet. In an aspect, the at least one camera maycapture emitted and/or reflected light. The image-capture device caninclude one or more electronic image sensors, e.g., photodiodes,photoresistors, charge-coupled devices (CCD), and/or complementary metaloxide semiconductor (CMOS) devices. For example, a CCD camera system canbe used to image luminescence, e.g., chemiluminescence, on a solidsubstrate (e.g., GeneGnome5, Syngene USA, Fredrick Md.). In an aspect,the image-capture device includes a single-shot capture device with oneCCD with a Bayer filter mosaic or three separate image sensors, whichare exposed to the same image via a beam splitter. In an aspect, theimage-capture device includes a multi-shot capture device. For example,a single CCD sensor may obtain additive color information by capturingan image three times, each with a different filter (e.g., red, green,and blue). For example, the CCD sensor may capture images as it is movedto various locations on the focal plane and a high resolution compositeimage “stitched” together. In an aspect, the image-capture deviceincludes a scanning device in which the sensor moves across the focalplane. For example, the camera can include a rotating line camera with alinear CCD array to assemble a high resolution digital image as thecamera rotates. Camera can include an area array of CCD or CMOS sensors.Camera can include a linear array of CCD (monochrome) or 3-strip CCDwith color filters.

In an aspect, image-capture device 720 includes at least one scanningdevice. Non-limiting examples of scanners include optical scanners,fluorescence scanners, acoustic scanners, electrical scanners,electromagnetic scanners, or magnetic scanners. In an aspect, thescanner includes an energy-emitting mechanism, e.g., a light source or alaser, and circuitry to scan the inner surface of a skin-coveringmaterial with directed energy, e.g., light of a specified wavelength, todetect one or more signals emitted from the inner surface ofskin-covering material and to transform the one or more detected signalsinto a digital output. In an aspect, the one or more signals emittedfrom one or more of the plurality of signal-generating complexes areindicative of the identity and/or spatial distribution of at least onetype of microbe associated with the skin surface of the individual.

In an aspect, image-capture device 720 includes a colorimetric scannerconfigured to detect color emitted from one or more of the plurality ofsignal-generating complexes in response to at least one type of microbe.For example, the colored signal may arise from a chromogenic reaction,examples of which have been described above herein. An example of acommercially available colorimetric scanner includes SpotWare™Colorimetric Microarray Scanners (Arrayit® Corporation, Sunnyvale,Calif.).

In an aspect, image-capture device 720 includes a fluorescence scanningdevice. In an aspect, the fluorescence scanning device can include fixedexcitation/emission wavelengths based on the use of standardcommercially available fluorescent dyes in the green, red, and nearinfrared wavelengths. For example, the fluorescence scanning device caninclude a two color scanner for scanning at two distinct wavelengths orwavelength bands. In an aspect, the fluorescence scanning device caninclude adjustable excitation/emission wavelengths, e.g., with one ormore excitation sources and filters to adjust the excitation/emissionwavelengths. Non-limiting examples of fluorescent scanners includeFluoroimage 595 or ImageQuant (GE Healthcare Life Sciences, Piscataway,N.J.), Tecan fluorescence scanners (Invitrogen, Carlsbad, Calif.),SureScan Microarray Scanner (Agilent Technologies, Inc., Santa Clara,Calif.), InnoScan® (Innopsys Inc., Chicago, Ill.). Additional examplesinclude fluorescence scanners with motorized stage for line scans acrossa surface (see, e.g., U.S. Pat. No. 6,371,370 or 8,385,619, which areincorporated herein by reference), and “stitching together” severalimage blocks to generate larger image (see, e.g., U.S. Pat. No.8,041,147, which is incorporated herein by reference).

In an aspect, image-capture device 720 can be configured to detect afluorescent response at a single wavelength of electromagnetic energy,at two wavelengths of electromagnetic energy, at multiple wavelengths ofelectromagnetic energy, or over extended-spectrum electromagneticenergy. In an aspect, the image-capture device can be configured todetect excitation energy. In an aspect, the image-capture device can beconfigured to detect a cumulative (optionally fluorescent) response overa time interval. In an aspect, the image-capture device can beconfigured to detect a (optionally fluorescent) response at a specifictime interval and/or at a specific time. In an aspect, the image-capturedevice can be configured to detect a time-dependent (optionallyfluorescent) response. In illustrative examples, the cumulative responseis determined over milliseconds, seconds, and/or minutes followingexcitation. In an aspect, the response is detected over millisecond,second, and/or minute time intervals following excitation. In an aspect,the response is detected approximately femtoseconds, picoseconds,nanoseconds, milliseconds, seconds, and/or minutes after excitation.

In an aspect, image-capture device 720 includes one or more imagingsensors including, but not limited to, one or more piezo transducers,one or more MEMS device, one or more cavity resonators, one or moremagneto resistive sensors, one or more magnetic field sensors, and/orone or more thermal sensors. In an aspect, image-capture device 720includes one or more electromagnetic energy sensors, one or moreacoustic sensors, one or more photodetectors, one or more radiofrequencyantennae, one or more magnetic energy sensors, one or more thermalsensors, and/or one or more electrical energy sensors. The one or moreelectromagnetic energy sensors can include one or more optical sensorsincluding, but not limit to, sensors configured to detect near infrared,ultraviolet, fluorescence, and/or visual light emitted by the at leastone type of signal-generating element.

In an aspect, image-capture device 720 includes components formicro-scanning in which a single CCD sensor with a Bayer filter is movedover the focus plane of the lens to “stitch” together a higherresolution image than the CCD would allow otherwise. In an aspect, themicro-scanning device includes a micro laser scanning device. See, e.g.,Seidl et al. (2006) International Society for Photogrammetry and RemoteSensing. Volume XXXVI Part 5. Sep. 25-27, 2006, Dresden Germany.

In an aspect, image-capture device 720 includes a three-dimensionalscanning device. Non-limiting examples of three-dimensional scanningdevices include NextEngine 3D Scanner (NextEngine, Inc., Santa Monica,Calif.), Handyscan 3D (Creaform USA Inc., Newark, Del.), or KonicaMinolta 3D scanners (Konica Minolta, Ramsey, N.J.).

In an aspect, image-capture device 720 includes a confocal laserscanner. In an aspect, the confocal laser scanner can include a handheldconfocal laser scanning microscope (e.g., VIVASCOPE 3000, MAVIG GmbH,Munich, Germany). In an aspect, the confocal laser scanner includes aMEMS confocal laser scanner. See, e.g., Murakami et al. (2003) The 12thInternational Conference on Solid State Sensors, Actuators andMicrosystems, Boston, Jun. 8-12, 2003, pp. 587-590, which isincorporated herein by reference.

In an aspect, image-capture device 720 includes a light source and adetector for measuring reflected and/or absorbed light. In an aspect,the image-capture device measures changes in refractive index on thesurface of the skin-covering material. The inner surface can beilluminated with a light source. Resonance occurs at a specific angle ofincident light. See, e.g., Barlen, et al. (2007) Sensors, 7:1427-1446;and Kashyap & Nemova (2009) J. Sensors:Article ID 645162, which areincorporated herein by reference.

In an aspect, image-capture device 720 includes a spectrometer orspectrophotometer. In an aspect, the spectrophotometer includes a fiberoptic spectrophotometer (from, e.g., Ocean Optics, Dunedin Fla.). In anaspect, the image-capture device includes a means of vibrationalspectroscopy. Examples of vibrational spectroscopy include, but are notlimited to, Fourier transform infrared (FTIR) spectroscopy andmicro-Raman spectroscopy. Raman spectroscopy can further includeUV-resonance Raman spectroscopy, surface enhanced Raman scattering, ortip-enhanced Raman scattering. See, e.g., Harz et al. (2009) Cytometry A75:104-113, which is incorporated herein by reference.

In an aspect, image-capture device 720 includes a light source, adigital projector, a CCD camera and a computing device forimage-processing for spatial frequency domain imaging, a wide fieldoptical technique. In an aspect, image-capture device 720 includes alens-free imaging system. See, e.g., Kim et al. (2012) J. Lab.Automation 17:43-49, which is incorporated herein by reference. In anaspect, one or more of the plurality of signal-generating complexesinclude one or more label-free optical biosensors that incorporate otheroptical methodologies, e.g., interferometers, waveguides, fibergratings, ring resonators, and photonic crystals. See, e.g., Fan, et al.(2008) Anal. Chim. Acta 620:8-26, 2008, which is incorporated herein byreference.

In an aspect, image-capture device 720 includes a type of flatbedcommercial scanner. For example, a flatbed commercial scanner can beused to image visible color emitted from one or more of the plurality ofsignal-generating complexes in response to at least one type of microbe.In an aspect, a commercial flatbed scanner can be combined with alaser-directed energy source and one or more lens to create a gigapixelinline digital holographic microscope capable of scanning a 297 mm by210 mm area, as described in Shimobaba et al. (2013) Optical Society ofAmerica. arXiv:1305.6084v1 [physics.optics] 27 May 2013, which isincorporated herein by reference. In an aspect, the scanner includes amechanical means for feeding the skin-covering material into thescanning device so as to scan the inner surface of the skin-coveringmaterial in parts.

In an aspect, image-capture device 720 can capture radioactivity emittedfrom a signal-generating complex that is radioactive. Examples ofmethods for detecting radioactivity include, but are not limited to,gas-filled tube detectors, e.g., Geiger counters; scintillation crystaldetectors; and solid-state semiconductor detectors. In an aspect, theone or more radioactivity sensors are one or more of a scintillationcrystal detector made from a material that fluoresces or emits lightwhen hit by radiation particles. The fluorescence or light can bemeasured using one or more of a light capture device, e.g., aphotomultiplier or photodiode. In an aspect, the one or moreradioactivity sensors are one or more of a microdosimeter. Amicrodosimeter for wireless measurement of radioactivity in vivo hasbeen described and is configured to detect ionizing radiation using aparallel plate capacitor to form a passive LC resonator. See, e.g., Son& Ziaie. IEEE Trans. Biomed. Eng. 55:1772-1775, 2008, which isincorporated herein by reference.

In an aspect, image-capture device 720 can capture magnetic signalsemitted from a signal-generating complex that is magnetic. In an aspect,the image-capture device can include one or more MEMS magnetic sensorssuch as described in Lee, et al. Magnetics Conference, 2006. INTERMAG2006. IEEE International, which is incorporated herein by reference.

In an aspect, image-capture device 720 can capture one or more signalsemitted or reflected directly from the at least one type of microbebound to the at least one specific microbe-binding element of thesignal-generating complex. In an aspect, the one or more signals emittedor reflected directly from the at least one type of microbe can be usedto complement the information received from the signal-generatingcomplexes, e.g., conformation of the identity of the type of microbeinteracting with the signal-generating complex. In an aspect, the one ormore signals emitted or reflected from the at least one type of microbeare representative of one or more properties of the at least one type ofmicrobe. The one or more properties can include one or more inherentproperties or characteristics of the at least one type of microbe thatare measureable by the image-capture device. In an aspect, the one ormore properties of the at least one type of microbe can include at leastone of an optical property, autofluorescence property, an infraredspectral property, a reflective property, a light scattering property,or an opacity property of the at least one type of microbe. In anaspect, the one or more properties of the at least one type of microbecan include one or more of a size, a morphological property, or aphysical feature. For example, the image-capture device can beconfigured to detect by optical or other means the shape, outline,and/or periphery of the at least one type of microbe on the innersurface of the skin-covering material.

In an aspect, image-capture device 720 includes circuitry configured tocapture at least one image of at least one first portion of the innersurface of skin-covering material 710 and at least one second portion ofthe inner surface of skin-covering material 710 adjacent to the at leastone first portion, and generate a composite image including the at leastone image of the at least first portion of the inner surface ofskin-covering material 710 and the at least one image of the at leastone second portion of the inner surface of skin-covering material 710.In an aspect, image-capture device 720 includes a feeding mechanism andan imaging surface sized to accommodate at least a portion ofskin-covering material 710, wherein the feeding mechanism is configuredto feed in the at least a portion of skin-covering material 710 onto theimaging surface. For example, the feeding mechanism can include one ormore rollers configured to feed at least a portion of a skin-coveringmaterial into an imaging surface associated with the image-capturedevice. For example, the feeding mechanism may include aspects of apaper feeding mechanism, e.g., including pickup and feed rollers. In anaspect, image-capture device 720 may further include a feeding mechanismfor removing the skin-covering material 710 from the imaging surface.For example, image-capture device 720 may have an input feedingmechanism on one side of the device and an output feeding mechanism onanother side of the device. For example, image-capture device 720 mayinclude a feeding mechanism, e.g., rollers, that rotate one direction tobring the skin-covering material into the device and that rotate in theopposite direction to push the skin-covering material out of the device.

In an aspect, image-capture device 720 includes a hand-heldimage-capture device. For example, image-capture device 720 can includea hand-held camera. In an aspect, image-capture device 720 and computingdevice 730 including the processor are incorporated into a single unit.For example, image-capture device 720 and computing device 730 can beincorporated into a personal electronic device, e.g., a smart phonedevice. In an aspect, image-capture device 720 is in wirelesscommunication with computing device 730. In an aspect, image-capturedevice 720 and computing device 730 including the processor areincorporated into an interactive kiosk.

Returning to FIG. 7, system 700 further includes computing device 730including a processor and operably coupled to image-capture device 720.Computing device 730 can take various forms or be part of an object, andcan include, but not limited to, a computer, a laptop computer, apersonal electronic device, a dedicated computing device, a limitedresource computing device, a wireless communication device, a mobilewireless communication device, a handheld electronic writing device, atablet, a digital camera, a scanner, a cell phone, a PDA, an electronictablet device, or any other like device that takes information as aninput and gives it back to the end-users. Computing device 730 caninclude a digital single processor, ASIC, microprocessor, or other typeof processor operating on a system such as a personal computer, server,a router, of other device capable of processing data including networkinterconnection device. In an aspect, computing device 730 andimage-capture device 720 are incorporated into a single unit. In anaspect, computing device 730 is part of a kiosk.

Computing device 730 further includes circuitry configured to receivethe digital output from image-capture device 720 including theinformation associated with the at least one property and the spatialdistribution of the imaged one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to theat least one type of microbe; compare the properties of the imaged oneor more signals emitted from the one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe with a database of emitted signals of referencesignal-generating complexes; and generate digital spatial profile 770 ofthe at least one type of microbe based on the spatial distribution ofthe imaged one or more signals emitted from the one or more of theplurality of signal-generating complexes in response to the at least onetype of microbe.

In an aspect, computing device 730 includes circuitry configured toverify an identity of the at least one type of microbe. In an aspect,computing device 730 includes circuitry configured to compare theproperties of the imaged one or more signals emitted from the one ormore of the plurality of signal-generating complexes with the databaseof emitted signals of reference signal-generating complexes. In anaspect, the database includes signal properties for referencesignal-generating complexes that emit signals in response to at leastone specific microbe. For example, computing device 730 can include adatabase containing a reference library of signal-generating complexesand associated autofluorescence properties at given excitationwavelengths. For example, computing device 730 can include a databasecontaining a reference library of signal-generating complexes andassociated optical, fluorescence, magnetic, acoustic, infrared spectral,electromagnetic, or electrical properties. For example, computing device730 can include a database containing a reference library ofsignal-generating complexes and associated properties such aswavelength, frequency, and/or amplitude. In an aspect, computing device730 includes one or more algorithms to process the digital outputprovided by the image-capture device. For example, the one or morealgorithms can include an algorithm for assessing the number of microbesin an image field. See, e.g., Selinummi et al., (2005) BioTechniques29:859-863, which is incorporated herein by reference.

In an aspect, the database of emitted signals of referencesignal-generating complexes includes emitted signals of matched sets ofspecific signal-generating elements operably coupled to specificmicrobe-binding elements that form specific signal-generating complexesand are configured to emit a specific signal in response to a specifictype of microbe. For example, computing device 730 can include adatabase or lookup table including reference signal properties formatched sets of signal-generating elements and specific microbe-bindingelements. For example, the database or lookup table can includeexcitation and emission spectra for one or more fluorescentsignal-generating elements. For example, the database can include colorwavelength information for chromogenic signal-generating elements. Forexample, the database can include radio frequencies for RFID tags. Forexample, the database can include infrared or FTIR spectral informationfor specific signal-generating elements. In an aspect, the databaseincludes signal properties for known signal-generating elements operablylinked to known specific microbe-binding elements such that if aspecific signal is detected, the system will know that a specificmicrobe is present. For example, the database may include signalproperties for Cy3 (approximately 570 nm emission) operably linked to anantibody against Propionibacterium acnes and signal properties for Cy5(approximately 670 nm emission) operably linked to an antibody againstStaphylococcus aureus. Detection of yellow-green signal properties wouldbe indicative of Cy3 and therefore the presence of Propionibacteriumacnes while detection of red signal properties would be indicative ofCy5 and therefore the presence of Staphylococcus aureus.

In an aspect, computing device 730 includes circuitry configured tocompare the generated digital spatial profile with a reference digitalspatial profile. In an aspect, the reference digital spatial profileincludes a historical digital spatial profile previously acquired forthe individual. For example, the reference digital spatial profile caninclude a historical digital spatial profile previously acquired for theindividual at a previous point in time, e.g., 1 to 24 hours previous, 1to 30 days previous, 1 to 12 months previous, and/or 1 to 30 yearsprevious. For example, the reference digital spatial profile can includea historical digital spatial profile previously acquired for theindividual before and/or after initiating a treatment regimen. Forexample, the reference digital spatial profile can include a historicaldigital spatial profile previously acquired for the individual beforeand/or after the onset of a skin condition, e.g., acne, psoriasis, oreczema. In an aspect, the reference digital spatial profile includes oneor more digital spatial profiles from at least one other individual. Forexample, the reference digital spatial profile may represent an averaged“normal” digital spatial profile. For example, the reference digitalspatial profile may represent an optimal profile based on an averaged“normal.” For example, the reference digital spatial profile mayrepresent the digital spatial profile of a celebrity or other suchindividual whose skin the individual admires and wishes to emulate byattaining the same microbiotic profile.

In an aspect, computing device 730 includes circuitry configured togenerate a recommended treatment regimen based on the comparison of thegenerated digital spatial profile with the reference digital spatialprofile. For example, comparing a recent digital spatial profile with ahistorical digital spatial profile may indicate an increase in anundesirable type of bacteria and as such the computing device cangenerate a recommended treatment regimen including antibiotic use,changes in diet, use of probiotics, and/or cleansing recommendations. Inan aspect, the recommended treatment regimen is designed to maintainand/or modify the type and/or distribution of microbes on the skinsurface of the individual. The recommended treatment regimen can includeuse of an anti-microbial agent, e.g., antibiotic or fungicide; use of acleaning regimen, e.g., type of soap, abrasive, astringent, and thelike; use of a probiotic, e.g., adding back bacteria or other microbesthat contribute to a healthy skin condition; change in a diet, e.g.,increased fluids, omitting certain foods, and the like; and/orrecommended cosmetic products, e.g., non-comedogenic products,microbe-compatible foundations or other make-up products, moisturizersor other skin creams, and the like. Computing device 730 furtherincludes circuitry to report to a user the recommended treatmentregimen.

In an aspect, computing device 730 further includes circuitry configuredto generate a digital alignment of the generated digital spatial profilewith a digital image of the skin surface of the individual covered bythe inner surface of the skin-covering material. One or more digitalimages of the skin surface of the individual can be captured, e.g., witha digital camera, before and/or after placement of the skin-coveringmaterial onto the skin surface. One or more registration marks on theskin-covering material may be used to register the skin-coveringmaterial relative to landmarks on the skin surface of the individual,the landmarks incorporated into the digital image of the skin surface.One or more registration marks on the skin-covering material can be usedto align with one or more landmarks on the skin surface. The one or morelandmarks on the skin surface can include one or more of pigmentation,pigmented areas, tattoos, skin texture patterns, blemishes, scars,anatomical features, or subsurface blood vessels associated with theskin surface. In an aspect, the one or more registration marks areincorporated into the manufacture of the skin-covering material based onthe presence of landmarks in the one or more digital images of the skinsurface used to form the skin-covering material. In an aspect, the oneor more registration marks can be added, e.g., with a pen or othermarking device, while the skin-covering material is on the skin-surfaceof the individual.

In an aspect, computing device 730 includes circuitry configured todetect one or more features depicted in the digital images, e.g., thephysical landmarks, and match these features with features in thedigital spatial profile, e.g., the registration marks. Features and therelationships between them may be detected using any of a number offeature-based methods including, but not limited to, segmentationmethods, distance transform, affinely invariant neighborhoods, Harriscorner detection, Maximally Stable External Regions, Canny detector,Laplacian of Gaussian, elastic contour extraction, existing edgedetection, line intersections, local extrema of wavelet transform,inflection points of curves, and the like. Computing device 730 includescircuitry to match the features detected in the one or more images ofskin surface of the individual with features in the digital spatialprofile using one or more feature-matching methods, non-limitingexamples of which include Euclidean distance matching, invariantmoments, nearest neighbor based matching, correlation-like methods,Fourier methods, mutual information methods, optimization methods.Further non-limiting examples include methods using spatial relations,e.g., graph matching algorithms, methods using invariant descriptors,and relaxation methods. The following references are incorporated byreference and include descriptions of computational methods for imageregistration: Szeliski Foundations and Trends in Computer Graphics andVision, Vol. 2, No. 1 (2006) 1-104, Zitova & Flusser Image VisionComputing (2003) 21:977-1000.

In an aspect, computing device 730 further includes circuitry configuredto generate a personalized microbe profile from the generated digitalalignment, the personalized microbe profile including at least one ofthe identity of the at least one type of microbe and a spatialdistribution of the identified at least one type of microbe on the skinsurface of the individual. In an aspect, computing device 730 includescircuitry to report to a user the generated personalized microbeprofile. In an aspect, the user includes the individual, e.g., theindividual for whom the personalized microbe profile is generated. In anaspect, the user includes a service-provider, e.g., a medicalprofessional or cosmetologist who performs the steps to generate thepersonalized microbe profile for an individual. In an aspect, the userincludes an interested third party, e.g., the manufacturer of theskin-covering material and/or system, a third-party payer such as aninsurance company, or a researcher.

In an aspect, computing device 730 includes circuitry configured toprovide a visual representation of the personalized microbe profile on adisplay. In an aspect, the display is operably coupled to computingdevice 730. For example, a visual representation of an individual'spersonalized microbe profile may be shown on a display of a computingdevice in an office of a medical professional or cosmetologist. Forexample, a visual representation of an individual's personalized microbeprofile may be shown on display of a kiosk or at a cosmetic counter. Inan aspect, the display is operably coupled to a second computing device.For example, the personalized microbe profile may be available on adisplay associated with a hand-held device, e.g., a personal computingdevice such as a smartphone device.

In an aspect, computing device 730 includes circuitry configured toprovide a printout to a user, the printout including the personalizedmicrobe profile. The printout can include textual description and/orvisual representation of the personalized microbe profile. For example,the printout may provide the personalized microbe profile as a textualdescription, e.g., identification of the at least one type of microbe onthe skin surface of the individual and generally where the microbes aredistributed, e.g., the nose area, the “T-zone,” the forehead, and thelike. For example, the printout may provide the personalized microbeprofile as a hardcopy version of the visual representation shown on adisplay. In an aspect, the printout may further include a recommendedtreatment regimen intended to maintain and/or modify the types anddistribution of microbes on the skin surface of the individual.

In an aspect, computing device 730 includes circuitry configured toexport information regarding the personalized microbe profile to atleast one second computing device. For example, the personalized microbeprofile may be generated on a first computing device, e.g., in aservice-provider's office, and subsequently downloaded to one or morecomputing devices accessible by the individual, e.g., a home computer ora smartphone device. For example, the personalized microbe profile maybe generated by a computing device associated with a kiosk andsubsequently downloaded to one or more computing devices accessible bythe individual. In an aspect, the at least one second computing deviceis associated with a retailer capable of providing a recommendedtreatment regimen, e.g., a pharmacy, a cosmetic counter, or otherretailer. In an aspect, the at least one second computing device isassociated with a manufacturer, e.g., the manufacturer of theskin-covering material and/or a component of a treatment regimen. In anaspect, the at least one second computing device is associated with athird party payer, e.g., an insurance company. In an aspect, the atleast one second computing device is associated with a research group.

In an aspect, computing device 730 includes circuitry configured togenerate a recommended treatment regimen based on an identity and aspatial distribution of the at least one type of microbe on the skinsurface of the individual; and report the generated recommendedtreatment regimen to a user. In an aspect, the recommended treatmentregimen is designed to maintain and/or modify the type and/ordistribution of microbes on the skin surface of the individual. Forexample, the circuitry can be configured to generate a recommendedtreatment regimen including an antimicrobial treatment based on thetypes of microbes present, e.g., antibiotics for bacteria, fungicide forfungus, or antiviral for a virus. For example, the circuitry can beconfigured to generate a recommended treatment regimen including a typeof skin cleaning process, e.g., a type of soap or antiseptic rinse,based on the identity and the distribution of the at least one type ofmicrobe. For example, the circuitry can be configured to generate arecommended treatment regimen including one or more probiotics orprebiotics to alter the microbe profile on the skin surface, e.g., tobalance beneficial microbes against harmful microbes. For example, thecircuitry can be configured to generate a recommended treatment regimenincluding a certain type of cosmetic product that is compatible with themicrobes present, e.g., helps to maintain beneficial microbes butdiscourages harmful microbes and can include probiotics and/orprebiotics. For example, the circuitry can be configured to generate arecommended treatment regimen including one or more medicaments, e.g.,hormone creams, oral hormones, or retinoid creams. Non-limiting examplesof components of a recommended treatment regimen include antimicrobialagents, cleansing products, cosmetic products, probiotics, prebiotics,medicaments, procedures (e.g., shaving or not in sensitive areas,applying warm compresses to open pores, use of a pore-opening orcleaning device, abrasion, and the like), and changes in diet. In anaspect, the circuitry can be configured to alert the individual as towhether the identity and the spatial distribution of the at least onetype of microbe warrants discussion with a medical professional. In anaspect, the computing device includes circuitry configured to report tothe user the recommended treatment regimen including via a display, aprintout, or exportation of data to another device, e.g., a personalhandheld device.

In an aspect, system 700 further includes at least one enhancingcomponent to enhance binding of the at least one type of microbe to theone or more of the plurality of signal-generating complexes. In anaspect, the enhancing component includes a thermal component, a vacuumcomponent, a humidity component, a chemical component, or a pressurecomponent. For example, a thermal component, e.g., heat at a temperaturecompatible with skin, may be used to open skin pores to allow access forsampling by the skin-covering material. For example, a vacuum componentassociated with the skin-covering material may be used to suction the atleast one type of microbe from the skin surface and onto the innersurface of the skin-covering material. For example, a humiditycomponent, e.g., pre-wetting the face or the skin-covering material, maybe used to create an aqueous environment for interaction with thesignal-generating complexes. For example, a pressure component, e.g.,applying equal pressure to the skin-covering material while it is on theskin surface of the individual may ensure equal capture andrepresentation of microbes from the skin surface.

In an aspect, the at least one enhancing component includes a chemicalenhancing component, non-limiting examples of which include at least oneof a skin-softener, a detergent, or a lysing compound. For example, thechemical enhancing component can be applied to the skin surface prior toapplying the skin-covering material. For example, the chemical enhancingcomponent may be included in the inner surface of the skin-coveringmaterial and makes contact with the skin upon applying the skin-coveringmaterial to the skin surface. In general, the chemical enhancingcomponent either enhances capture of microbes from the skin surface,e.g., enhancing accessibility, or enhances detection of one or morebiomolecules associated with the microbes. In an aspect, the enhancingcomponent includes at least one skin-softener, non-limiting examples ofwhich include emollients, moisturizers, lubricants, and/or oils.

In an aspect, the enhancing component includes a lysing compound to lysethe one or more microbes either directly on the skin surface or on theinner surface of the skin-covering material. The lysing compound allowsbiomolecules, e.g., proteins or nucleic acids, in the interior of themicrobe to be more accessible for detection. Non-limiting examples oflysing compounds includes urea, enzymes for lysing bacterial cell walls(e.g., lysozyme, labiase, lysostaphin, mutanolysis, achromopeptidase),and enzymes for lysing fungal, e.g., yeast, cell walls (e.g., kitalase,lyticase, chitinase, glucanase). One or more detergents or surfactantsmay also be used for lysing cells, non-limiting examples of whichinclude nonionic detergents, e.g., Triton X-100, Nonidet P-40, Tween 20;zwitterionic detergents, e.g., CHAPS; and ionic detergents, e.g., sodiumdodecyl sulfate.

FIG. 8 illustrates further embodiments of computing device 730 for usein a system for assessing the microbiota of skin. Computing device 730includes a processing unit 821, a system memory 822, and a system bus823 that couples various system components including the system memory822 to the processing unit 821. Processing unit 821 can include amicroprocessor, a central processing unit (CPU), a digital signalprocessor (DSP), an application-specific integrated circuit (ASIC), afield programmable gate entry (FPGA), or the like, or any combinationsthereof, and can include discrete digital or analog circuit elements orelectronics, or combinations thereof. In an aspect, the computing deviceincludes one or more ASICs having a plurality of pre-defined logiccomponents. In an aspect, the computing device includes one or more FPGAhaving a plurality of programmable logic commands.

The system bus 823 may be any of several types of bus structuresincluding a memory bus or memory controller, a peripheral bus, and alocal bus using any of a variety of bus architectures. By way ofexample, and not limitation, such architectures include IndustryStandard Architecture (ISA) bus, Micro Channel Architecture (MCA) bus,Enhanced ISA (EISA) bus, Video Electronics Standards Association (VESA)local bus, and Peripheral Component Interconnect (PCI) bus, also knownas Mezzanine bus.

Computing device 730 includes a user interface, e.g., one or more inputdevices 831 and/or output devices 839 for use by a user to interfacewith the computing device. The one or more input devices 831 can be usedto enter information into the computing device and may be integratedinto the computing device or may be one or more peripheral devicesoperably connected through a wired or wireless connection to thecomputing device. Non-limiting examples of input devices 831 include agraphical user interface, a display, a keyboard, a keypad, a trackball,a joystick, a touch-screen, a mouse, a microphone, an image scanner, adigital camera, a webcam, a light pen, a bar code reader, a fingerprintscanner, a retinal scanner, a game pad, a stylus pen a switch, a dial,or the like. In an aspect, the input device 831 is part of a kioskstructure.

The user interface may include a character, a key-based, or another userdata input via a keyboard or touch sensitive display. The user interfacemay include using a stylus (not shown). Moreover, the user interface isnot limited to an actual touch-sensitive panel arranged for directlyreceiving input, but may alternatively or in addition respond to anotherinput device such as a microphone. A user may enter commands andinformation into the computing device 730 through user input devices,such as a number of switches and buttons, illustrated as hardwarebuttons 844, connected to the system via a suitable interface 845. Inputdevices 831 may further include a touch-sensitive display with suitableinput detection circuitry, illustrated as a display 832 and screen inputdetector 833. The output circuitry of the touch-sensitive display 832 isconnected to the system bus 823 via a video driver 837. Other inputdevices may include a microphone 834 connected through a suitable audiointerface 835, and a physical hardware keyboard 810. Output devices mayinclude at least one of the display 832, or a projector display 836.Input device 831 may further include a microphone, keyboard, or pointingdevice, commonly referred to as a mouse, trackball, or touch pad. Otherinput devices may include at least one of a touch sensitive display,joystick, game pad, satellite dish, and scanner.

The user interface includes one or more output devices 839 over whichprocessed information is viewed as output results and may be integratedinto the computing device or may be one or more peripheral devicesoperably connected through a wired or wireless connection to thecomputing device. Non-limiting examples of output devices 839 includebut are not limited to television screens, computer monitors, liquidcrystal displays, audio speakers, audio headphones, and printers. In anaspect, the computing device 730 may include at least one speaker 838connected through a suitable audio interface 835. The one or more outputdevices 839 can be used to report to a user an identification and/or aspatial distribution of at least one type of microbe on a skin surfaceof an individual. In an aspect, the input/output devices includeimage-capture device 310 connected through a wired or wirelessconnection to the computing device.

In an aspect, the one or more input/output devices are connected to theprocessing unit of the computing device through one or more user inputinterfaces that are coupled to the system bus, but may be connected byother interfaces and bus structures, such as a parallel port, game port,or a universal serial bus (USB). For example, input devices 831 oroutput devices 839, may be connected to the processing unit 821 througha USB port 840 and USB port interface 841, to the system bus 823.Alternatively, the other external input devices 831 and output devices839 may be connected by other interfaces, such as a parallel port, gameport or other port. The computing device 730 may further include or becapable of connecting to a flash card memory (not shown) through anappropriate connection port (not shown). The computing device 730 mayfurther include or be capable of connecting with a network through anetwork port 842 and network interface 843, and through wireless port846 and corresponding wireless interface 847 may be provided tofacilitate communication with other peripheral devices, for example, thescanning device. It will be appreciated that the various components andconnections shown are examples and other components and means ofestablishing communication links may be used.

In an aspect, image-based applications such as viewers and/or toolkits(e.g., Insight Segmentation and Registration Toolkit (ITK)), areincorporated for further intake of information. In an aspect, CADimplementations, image segmentation, or other image analysis algorithmsmay allow processing of images received from an image capture device.

The system memory includes read-only memory (ROM) 824 and random accessmemory (RAM) 825. A basic input/output system (BIOS) 826, containing thebasic routines that help to transfer information between sub-componentswithin computing device 730, such as during start-up, is stored in theROM 824. A number of program modules may be stored in the ROM 824 or RAM825, including an operating system 827, one or more application programs828, other program modules 829 and program data 830.

Computing device 730 includes computer-readable media products and mayinclude any media that can be accessed by the computing device 730including both volatile and nonvolatile media, removable andnon-removable media. By way of example, and not of limitation,computer-readable media may include non-transitory signal-bearing media.By way of example, and not of limitation, computer-readable media mayinclude computer storage media. By way of further example, and not oflimitation, computer-readable media may include a communication media.

Communication media may typically embody computer-readable instructions,data structures, program modules, or other data in a modulated datasignal such as a carrier wave or other transport mechanism and includeany information delivery media. The term “modulated data signal” means asignal that has one or more of its characteristics set or changed insuch a manner as to encode information in the signal. By way of example,and not limitation, communication media include wired media, such as awired network and a direct-wired connection, and wireless media such asacoustic, RF, optical, and infrared media.

Computing device 730 may also include other removable/non-removable,volatile/nonvolatile computer storage media products implemented in anymethod or technology for storage of information such ascomputer-readable instructions, data structures, program modules, orother data. For example, such media includes a non-removablenon-volatile memory interface (hard disk interface) 845 reads from andwrites for example to non-removable, non-volatile magnetic media, or aremovable non-volatile memory interface 850 that, for example, iscoupled to a magnetic disk drive 851 that reads from and writes to aremovable, non-volatile magnetic disk 852, or is coupled to an opticaldisk drive 855 that reads from and writes to a removable, non-volatileoptical disk 856, such as a CD ROM. Other removable/nonremovable,volatile/non-volatile computer storage media that can be used in theexample operating environment include, but are not limited to, magnetictape cassettes, magnetic tape, magnetic disk storage, optical diskstorage, memory cards, flash memory cards, DVDs, electrically erasableprogrammable read-only memory (EEPROM), digital video tape, solid stateRAM, and solid state ROM or any other medium which can be used to storethe desired information and which can be accessed by the computingdevice 730. The hard disk drive 257 is typically connected to the systembus 823 through a non-removable memory interface, such as the interface845, and magnetic disk drive 851 and optical disk drive 855 aretypically connected to the system bus 823 by a removable non-volatilememory interface, such as interface 850. In an aspect, computing device730 includes a computer-readable media drive or memory slot configuredto accept non-transitory signal-bearing medium (e.g., computer-readablememory media, computer-readable recording media, or the like). In anaspect, a computer storage media may include a group of computer storagemedia devices. In an aspect, a computer storage media may include aninformation store. In an aspect, an information store may include aquantum memory, a photonic quantum memory, or atomic quantum memory.Combinations of any of the above may also be included within the scopeof computer-readable media.

In an aspect, a program or set of instructions for causing a system toexecute any of the disclosed methods can be stored on, for example, acomputer-readable recording medium (CRMM), a non-transitorysignal-bearing medium, or the like. Non-limiting examples ofsignal-bearing media include a recordable type medium such as magnetictape, floppy disk, a hard disk drive, Compact Disc (CD), a Digital VideoDisk (DVD), Blu-Ray Disc, digital tape, computer memory, or the like, aswell as transmission type medium such as a digital and/or analogcommunication medium (e.g., fiber optic cable, waveguide, wiredcommunications link, wireless communication link). Further non-limitingexamples of signal-bearing media include, but are not limited to,DVD-ROM, DVD-RAM, DVD+RW, DVD-RW, DVD-R, DVD+R, CD-ROM, Super Audio CD,CD-R, CD+R, CD+RW, CD-RW, Video Compact Discs, Super Video Discs, flashmemory, magnetic tape, magneto-optic disk, MINIDISC, non-volatile memorycard, EEPROM, optical disk, optical storage, RAM, ROM, system memory,web server, cloud, or the like.

The drives and their associated computer storage media discussed aboveprovide storage of computer-readable instructions, data structures,program modules, and other data for the computing device 730.

The computing device may operate in a networked environment usinglogical connections to one or more remote computers, such as a remotecomputer 880. The remote computer 880 may be a personal computer, aserver, a router, a network PC, a peer device, or other common networknode, and typically includes many or all of the elements described aboverelative to the computing device 730. The network logical connectionsinclude a local area network (LAN) and a wide area network (WAN), andmay also include other networks such as a personal area network (PAN)(not shown). Such networking environments are commonplace in offices,enterprise-wide computer networks, intranets, and the Internet.

When used in a networking environment, the computing device is connectedto the network 871 through a network interface, such as the networkinterface 870, the modem 872, or the wireless interface 893. The networkmay include a LAN network environment, or a WAN network environment,such as the Internet. In a networked environment, program modulesdepicted relative to the computing device 730, or portions thereof, maybe stored in a remote memory storage device. By way of example, and notlimitation, remote application programs 885 as residing on computermedium 881. It will be appreciated that the network connections shownare examples and other means of establishing communication link betweenthe computers may be used.

In some embodiments, the computing device includes one or more modulesoptionally operable for communication with one or more input/outputcomponents that are configured to relay user output/input. In an aspect,a module includes one or more instances of electrical,electromechanical, software-implemented, firmware-implemented, or othercontrol devices. Such devices include one or more instances of memory,computing devices, antennas, power or other supplies, logic modules orother signaling modules, gauges or other such active or passivedetection components, piezoelectric transducers, shape memory elements,micro-electro-mechanical systems (MEMS) elements, or other actuators.

In certain instances, one or more elements of the computing device 730may be deemed not necessary and omitted. In other instances, one or moreother components may be deemed necessary and added to computing device730.

FIG. 9 illustrates aspects of a system for assessing microbiota of skinincluding a pre-formed skin-covering material that includes a pluralityof signal-generating complexes. System 900 includes device 300 ofpre-formed skin-covering material 310, image-capture device 720, andcomputing device 730. Pre-formed skin-covering material 310 includesinner surface 320 and outer surface 330, inner surface 320 substantiallyconforming in shape to a topography of a skin surface of an individual.Inner surface 320 further includes attached thereto a plurality ofsignal-generating complexes, each of the plurality of signal generatingcomplexes including specific microbe-binding element 350 operablycoupled to either signal-generating element in a first state 340 a orsignal-generating element in a second state 340 b. Signal-generatingelement in a first state 340 a is capable of converting tosignal-generating element in a second state 340 b in response to atleast one microbe. In an aspect, conversion from the first state to thesecond state results in a change in signaling capability, e.g., nosignal in response to directed energy to a detectable signal in responseto directed energy. In an aspect, conversion from the first state to thesecond state results in a detectable color change, e.g., from colorlessto blue. Signal-generating element in a second state 340 b is operablycoupled to specific microbe-binding element 350 to which microbe 910 isbound. Signal-generating element in a second state 340 b emits one ormore signals 920 in response to directed energy 750 from image-capturedevice 720 while signal-generating element in a first state 340 a doesnot emit one or more signals 920 in response to directed energy 750.Image-capture device 720 includes circuitry to transform one or moresignals 920 into a digital output including at least one property andspatial distribution of one or more signals 920. Computing device 730 isoperably coupled to image-capture device 720 through communication link725 and includes circuitry to receive the digital output fromimage-capture device 720. Computing device 730 further includescircuitry configured to compare the properties of one or more signals920 with a database of emitted signals of reference signal-generatingcomplexes and generate a digital spatial profile of microbe 910 on theinner surface of pre-formed skin-covering material 310 based on thespatial distribution of one or more signals 760.

FIG. 10 illustrates aspects of a system for assessing microbiota of skinincluding a pre-formed skin-covering material that includes a pluralityof signal-generating complexes of a first type and a plurality ofsignal-generating complexes of a second type. System 1000 includesdevice 400 of pre-formed skin-covering material 410, image-capturedevice 720, and computing device 730. Pre-formed skin-covering material410 includes inner surface 420 and outer surface 430, inner surface 420substantially conforming in shape to a topography of a skin surface ofan individual. Inner surface 420 further includes attached thereto aplurality of signal-generating complexes of a first type, each of theplurality of signal generating complexes of the first type includingsignal-generating element 440 operably coupled to specificmicrobe-binding element 450 and a plurality of signal-generatingcomplexes of a second type including signal-generating element 460operably coupled to specific microbe-binding element 470.Signal-generating element 440 emits one or more signals 1030 in responseto directed energy 760 from image-capture device 720 when microbe 1010is associated with operably coupled specific microbe-binding element450. Signal-generating element 460 emits one or more signals 1040 inresponse to directed energy 760 from image-capture device 720 whenmicrobe 1020 is associated with operably coupled specificmicrobe-binding element 470. Image-capture device 720 includes circuitryto transform one or more signals 1030 into a digital output including atleast one property and spatial distribution of one or more signals 1030and to transform one or more signals 1040 into a digital outputincluding at least one property and spatial distribution of one or moresignals 1040. Computing device 730 is operably coupled to image-capturedevice 720 through communication link 725 and includes circuitry toreceive the digital output from image-capture device 720. Computingdevice 730 further includes circuitry configured to compare theproperties of one or more signals 1030 and one or more signals 1040 witha database of emitted signals of reference signal-generating complexesand generate a digital spatial profile of microbe 1010 and 1020 on theinner surface of pre-formed skin-covering material 310 based on thespatial distribution of one or more signals 1030 and one or more signals1040, respectively. In an aspect, two or more types of microbes can bedistinguished using signal-generating complexes of two or more typesthat emit two or more signal types in response to the two or more typesof microbes.

FIG. 11 illustrates aspects of a system including a peelableskin-covering material including a plurality of signal-generatingcomplexes for assessing the microbiota of skin. System 1100 includespeelable skin-covering material 550, image-capture device 720, andcomputing device 730. Peelable skin-covering material 550 including aplurality of signal-generating complexes, each of the plurality ofsignal-generating complexes including at least one signal-generatingelement 520 operably coupled to at least one specific microbe-bindingelement 530 is formed from settable material 510 and substantiallyconforms in shape to a topography of a skin surface of individual 1110.Settable material 510 includes at least one material configured toundergo a phase change from a liquid or gelled phase to a flexible solidphase in response to an applied stimulus and includes the plurality ofsignal-generating complexes including at least one signal-generatingelement 520 operably coupled to at least one specific microbe-bindingelement 530.

Image-capture device 720 of system 1100 includes circuitry to capture atleast one image of the inner surface of peelable skin-covering material550 to image one or more signals 1130 emitted from one or more of theplurality of signal-generating complexes. In an aspect, one or moresignals 1130 are emitted in response to directed energy 1120.Image-capture device 720 further includes circuitry to transform thecaptured at least one image into a digital output including informationassociated with at least one property and a spatial distribution ofimaged one or more signals 1130.

Computing device 730 of system 1100 includes a processor and is operablycoupled to image-capture device 720 through communications link 725.Computing device 730 includes circuitry configured to receive digitaloutput from image-capture device 720 including the informationassociated with the at least one property and the spatial distributionof the one or more signals 1130 emitted from the one or more of theplurality of signal-generating complexes on the inner surface ofpeelable skin-covering material 550, compare the properties of the oneor more signals 1130 emitted from the one or more of the plurality ofsignal-generating complexes with a database of emitted signals ofreference signal-generating complexes, and generate digital spatialprofile 1140 of the at least one type of microbe based on the spatialdistribution of one or more signals 1130 emitted from the one or more ofthe plurality of signal-generating complexes. In an aspect, computingdevice 730 further includes circuitry to generate a digital alignment1150 of digital spatial profile 1140 of the at least one type of microbewith a digital image of a skin surface of individual 1110 covered bysettable material 510 prior to peeling. Digital alignment 1150 can bereported to a user of the system, e.g., individual 1110 or anotherindividual, to aid in determining a recommended treatment regimen tomaintain or alter the current types and spatial distribution of microbeson the skin surface of the individual.

FIGS. 12A, 12B, and 12C illustrate aspects of a system including apeelable skin-covering material and a plurality of signal-generatingcomplexes of a first type and a plurality of signal-generating complexesof a second type. System 1200 includes settable material 1220, peelableskin-covering material 1260, image-capture device 720, and computingdevice 730. FIG. 12A shows a cross-section through settable material1220 applied to skin surface 1210. Settable material 1220 includes atleast one material configured to undergo a phase change form a liquid orgelled phase to a flexible solid phase in response to an appliedstimulus. Settable material 1220 includes at least one of latex, gel,polymer, plastic, or resin. Settable material 1220 includes a pluralityof signal-generating complexes of a first type 1230 and a plurality ofsignal-generating complexes of a second type 1240. In an aspect, one ormore of the plurality of signal-generating complexes of a first type1230 includes at least one signal-generating element of a first typeoperably coupled to at least one specific microbe-binding element of afirst type, the at least one signal-generating element of the first typeconfigured to emit one or more signals of a first type in response to atleast one first type of microbe bound to the operably coupled at leastone specific microbe-binding element of the first type. In an aspect,one or more of the plurality of signal-generating complexes of a secondtype 1240 includes at least one signal-generating element of a secondtype operably coupled to at least one specific microbe-binding elementof a second type, the at least one signal-generating element of thesecond type configured to emit one or more signals of a second type inresponse to at least one second type of microbe bound to the operablycoupled at least one specific microbe-binding element of the secondtype.

FIG. 12B illustrates a cross-section through peelable skin-coveringmaterial 1260 formed from application of stimulus 1250 to settablematerial 1220. Stimulus 1250 can include at least one of air, a thermalstimulus, or an electromagnetic stimulus. Peelable skin-coveringmaterial 1260 includes the plurality of signal-generating complexes of afirst type 1230 and the plurality of signal-generating complexes of asecond type 1240. FIG. 12C illustrates a cross-section of peelableskin-covering material 1260 in contact with image-capture device 720. Atleast one of the plurality of signal-generating complexes of a firsttype 1230 emits one or more signals 1275 in response to microbe 1270 andat least one of the plurality of signal-generating complexes of a secondtype 1240 emits one or more signals 1285 in response to microbe 1280. Inan aspect, one or more signals 1275 and/or one or more signals 1285 areemitted and/or reflected in response to directed energy 1290 generatedfrom an energy-generating mechanism of image-capture device 720.Image-capture device includes circuitry to transform one or more signals1275 and one or more signals 1285 into a digital output includingproperties and spatial distributions of one or more signals 1275 and oneor more signals 1285. Computing device 730 is operably coupled toimage-capture device 720 through communication link 725 and includescircuitry to generate a digital spatial profile of microbe 1270 and ofmicrobe 1280 based on the spatial distribution of one or more signals1275 and one or more signals 1285, respectively, as described aboveherein.

FIG. 13 shows a flowchart of a method for assessing microbiota of theskin. The method includes receiving a digital output from animage-capture device, the digital output including informationassociated with at least one property and at spatial distribution of oneor more signals emitted from one or more of a plurality ofsignal-generating complexes associated with an inner surface of askin-covering material, the one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to atleast one type of microbe in block 1300; identifying the at least onetype of microbe by comparing the information associated with the atleast one property of the one or more signals emitted from the one ormore of the plurality of signal-generating complexes with a database ofsignal properties of reference signal-generating complexes in block1310; generating a digital spatial profile of the at least one type ofmicrobe based on the spatial distribution of the one or more signalsemitted from the one or more of the plurality of signal-generatingcomplexes in response to the at least one type of microbe in block 1320;and reporting to a user an identification and the digital spatialprofile of the identified at least one type of microbe in block 1330.

In an aspect, the method of FIG. 13 is implemented on a computingdevice. In an aspect, the method of FIG. 13 is implemented on computingdevice such as that described in FIG. 8. The computing device can takevarious forms or be part of an object, and can include, but not limitedto, a computer, a laptop computer, a personal electronic device, adedicated computing device, a limited resource computing device, awireless communication device, a mobile wireless communication device, ahandheld electronic writing device, a tablet, a digital camera, ascanner, a cell phone, a PDA, an electronic tablet device, or any otherlike device that takes information as an input and gives it back to theend-users. The computing device can include a digital single processor,ASIC, microprocessor, or other type of processor operating on a systemsuch as a personal computer, server, a router, of other device capableof processing data including network interconnection device. In anaspect, the computing device is part of a kiosk.

FIG. 14 shows further aspects of a method such as shown in FIG. 13. Inan aspect, receiving a digital output from an image-capture device caninclude receiving the digital output from at least one digital camera asillustrated in block 1400. Non-limiting examples of digital cameras havebeen described above herein. In an aspect, receiving a digital outputfrom an image-capture device can include receiving the digital outputfrom at least one scanning device as shown in block 1410. In an aspect,receiving the digital output from at least one scanning device includesreceiving the digital output from at least one active scanning device.For example, the scanning device can include an energy-generatingmechanism that generates directed energy, e.g., a laser, which is usedto elicit a response from one or more of the plurality ofsignal-generating complexes on the inner surface of the skin coveringmaterial. In an aspect, receiving the digital output from at least onescanning device includes receiving the digital output from at least onepassive scanning device. For example, the scanning device can passivelyreceive one or more signals, e.g., an optical signal, radioactive, ormagnetic signals, from one or more of the plurality of signal-generatingcomplexes. In an aspect receiving the digital output from at least onescanning device include receiving the digital output from athree-dimensional scanning device. In an aspect, receiving the digitaloutput from at least one scanning device includes receiving the digitaloutput from at least one of an optical scanning device, a fluorescencescanning device, an acoustic scanning device, or an electromagneticscanning device.

The method includes identifying the at least one type of microbe bycomparing the information associated with the at least one property ofthe one or more signals emitted from the one or more of the plurality ofsignal-generating complexes with a database of signal propertiesassociated with one or more reference signal-generating complexes. In anaspect, comparing the information associated with the at least oneproperty includes comparing at least one of an optical property as shownin block 1420. For example, the method can include comparing a change incolor with a reference color, e.g., colorless to violet, in response tothe at least one type of microbe. In an aspect, comparing theinformation associated with the at least one property includes comparingat least one of a fluorescence property as shown in block 1425. Forexample, the method can include comparing a fluorescent signal, e.g.,green fluorescence associated with fluorescein or Cy3, or a change influorescence, e.g., an intensity, in response at least one type ofmicrobe with a reference fluorescence or change in fluorescence. In anaspect, comparing the information associated with the at least oneproperty includes comparing at least one of an infrared spectralproperty as shown in block 1430. In an aspect, comparing the informationassociated with the at least one property includes comparing at leastone of an acoustic property as shown in block 1435. In an aspect,comparing the information associated with the at least one propertyincludes comparing at least one of a magnetic property as shown in block1440. In an aspect, comparing the information associated with the atleast one property includes comparing at least one of an electromagneticproperty as shown in block 1445. In an aspect, comparing the informationassociated with the at least one property includes comparing at leastone of an electrical property as shown in block 1450. In an aspect,comparing the information associated with the at least one propertyincludes comparing at least one of a wavelength as shown in block 1455.In an aspect, comparing the information associated with the at least oneproperty includes comparing at least one of a frequency as shown inblock 1460. In an aspect, comparing the information associated with theat least one property includes comparing at least one of an amplitude asshown in block 1465.

In an aspect, the method includes generating a recommended treatmentregimen based on the identification and the digital spatial profile ofthe identified at least one type of microbe; and reporting therecommended treatment regimen to the user, as shown in block 1470 ofFIG. 14. For example, the method can include generating a recommendedtreatment regimen that includes an antimicrobial treatment based on thetypes of microbes present, e.g., antibiotics for bacteria, fungicide forfungus, or antiviral for a virus. For example, the method can includegenerating a recommended treatment regimen that includes a skin cleaningprocess, e.g., a type of soap or antiseptic rinse, based on the identityand the distribution of the at least one type of microbe. For example,the method can include generating a recommended treatment regimen thatincludes a certain type of cosmetic product that is compatible with themicrobes present, e.g., helps to maintain good microbes but notencourage bad microbes and can include probiotics. Non-limiting examplesof treatment recommendations include antimicrobial agents, cleansingproducts, cosmetic products, procedures (e.g., shaving or not insensitive areas, applying warm compresses to open pores, use of apore-opening or cleaning device, abrasion, and the like). In an aspect,the method can include alerting the individual as to whether theidentity and the spatial distribution of the at least one type ofmicrobe warrants discussion with a medical professional. In an aspect,reporting the recommended treatment regimen to the user includesreporting the recommended treatment regimen via a display, a printout,or exportation of data to another device, e.g., a personal handhelddevice, or to another individual, e.g., a service provider or interestedthird party.

FIG. 15 shows further aspects of a method such as shown in FIG. 13. Inan aspect, the method includes generating at digital alignment of thedigital spatial profile of the identified at least one type of microbewith a digital image of a skin surface of an individual covered by theinner surface of the skin-covering material; generating a personalizedmicrobe profile for the individual from the generated digital alignment,the personalized microbe profile including the identification and aspatial profile of the identified at least one type of microbe on theskin surface of the individual; and reporting to the user thepersonalized microbe profile, as illustrated in block 1500. In anaspect, reporting to a user includes reporting to the individual, i.e.,the individual for whom the personalized microbe profile was generated.In an aspect, reporting to the user includes reporting to a serviceprovider, e.g., a medical practitioner, a cosmetologist, or otherservice provider, who prepares the personalized microbe profile for theindividual. In an aspect, reporting to the user includes reporting to athird party, e.g., an insurance company or the manufacturer of theskin-covering material and/or components of the system including theskin-covering material.

In an aspect, the method includes using one or more image registrationalgorithms to generate the digital alignment between the digital spatialprofile and the digital image of the skin surface of an individual. Inan aspect, the method includes aligning one or more registration marks,e.g., colored or fluorescent spots with one or more correspondinglandmarks from the skin surface captured by the digital image. Forexample, the method can include aligning one or more registration markson the digital spatial profile with one or more corresponding moles onthe skin surface of the individual. For example, the method can includealigning one or more registration marks on the digital spatial profilewith one or more corresponding marks placed on the skin surface of theindividual with a pen.

In an aspect, the method includes detecting one or more featuresdepicted in the digital images, e.g., the physical landmarks, and matchthese features with features in the digital spatial profile, e.g., theregistration landmarks. Features and the relationships between them maybe detected using any of a number of feature-based methods including,but not limited to, segmentation methods, distance transform, affinelyinvariant neighborhoods, Harris corner detection, Maximally StableExternal Regions, Canny detector, Laplacian of Gaussian, elastic contourextraction, existing edge detection, line intersections, local extremaof wavelet transform, inflection points of curves, and the like. Themethod further includes matching the features detected in the one ormore digital images of the skin surface with features in the digitalspatial profile using one or more feature-matching methods, non-limitingexamples of which include Euclidean distance matching, invariantmoments, nearest neighbor based matching, correlation-like methods,Fourier methods, mutual information methods, optimization methods.

In an aspect, the method includes providing a visual representation ofthe personalized microbe profile on a display, as illustrated in block1510. The display can include a display coupled to a computing device,wherein the computing device can take various forms or be part of anobject, and can include, but not limited to, a computer, a laptopcomputer, a personal electronic device, a dedicated computing device, alimited resource computing device, a wireless communication device, amobile wireless communication device, an electronic pen, a handheldelectronic writing device, a tablet, a digital camera, a scanner, anultrasound device, an x-ray machine, a non-invasive imaging device, acell phone, a PDA, an electronic tablet device, a medical apparatus, orany other like device that takes information as an input and gives itback to the end-users. In an aspect, the display is part of a kiosk thatincludes the image-capture device and the computing device.

In an aspect, the method includes providing a printout of thepersonalized microbe profile, as illustrated in block 1520. For example,the printout of the personalized microbe profile can include a text onlydescription of the identity and spatial profile of the identified atleast one type of microbe on the skin surface of the individual. Forexample, the printout of the personalized microbe profile can include acolor-coded diagram illustrating the identity and the spatial profile ofthe identified at least one type of microbe on the skin surface of theindividual. The color-coded information can be overlaid on an image ofthe skin surface of the individual. For example, the color-coded diagramcan be overlaid over an image of the individual's face, illustrating thedistribution of one or more types of microbes on the individual's face.

In an aspect, the method includes exporting the personalized microbeprofile to a computing device, as illustrated in block 1530. Forexample, the personalized microbe profile may be generated on a firstcomputing device, e.g., a service provider's office, operably coupled tothe image-capture device, e.g., in a service provider's office, andsubsequently exported to a second computing device, e.g., anindividual's home computer, a hand-held device, personal electronicdevice, or the like. For example, the personalized microbe profile maybe generated on a first computer in the individual's residence andsubsequently exported to a second computer associated with a serviceprovider, e.g., a medical practitioner's office, a pharmacy, or cosmeticcounter. In an aspect, the service provider may provide a recommendedtreatment regimen in response to receipt of an individual's personalizedmicrobe profile.

In an aspect, the method can include generating a recommended treatmentregimen based on the personalized microbe profile, and reporting therecommended treatment regimen to the user as shown in block 1540. Forexample, the method may include recommending a specific antibioticand/or antifungal regimen based on the personalized microbe profile. Forexample, the method may include recommending a skin-cleansing regimenbased on the personalized microbe profile. For example, the method mayinclude recommending a probiotic regimen based on the personalizedmicrobe profile. Non-limiting components of a recommended treatmentregimen have been described above herein.

In an aspect, the method includes comparing the personalized microbeprofile with a reference microbe profile, generating a recommendedtreatment regimen for the individual based on the comparison, andreporting the recommended treatment regimen to the user, as shown inblock 1550. In an aspect, the method can include comparing with areference microbe profile generated for the individual at a previouspoint in time, as shown in block 1560. The previous point in time caninclude days, months, and/or years prior to a current time point. Forexample, the method can include comparing the microbe profile with areference microbe profile generated when the individual was younger,allowing for analysis of the microbe profile as a function of age. Forexample, the method can include comparing the microbe profile with areference microbe profile generated for an individual prior to the onsetof a medical condition, e.g., acne, psoriasis, or eczema. For example,the method can include comparing the microbe profile with a referencemicrobe profile generated for an individual prior to treatment for askin condition, allowing for analysis of the microbe profile before andafter a treatment regimen.

In an aspect, the method can include comparing with a reference microbeprofile generated for one or more other individuals, as shown in block1570. For example, the method can include comparing the microbe profilewith a reference microbe profile that represents an optimal microbeprofile generated by averaging microbe profile information gathered froma number of other individuals. For example, the method can includecomparing the microbe profile with a reference microbe profile thatrepresents an optimal microbe profile generated from one or more otherindividuals with a complexion preferred by the individual. For example,the method can include comparing the microbe profile with referencemicrobe profile that represents a microbe profile from a celebrity witha complexion or skin properties preferred by the individual.

FIG. 16 illustrates aspects of a method for assessing microbiota ofskin. The method includes generating a recommended treatment regimenbased on comparing microbiota of a skin surface of an individual at twoor more points in time. The method includes receiving a first digitaloutput from an image-capture device at block 1600, the first digitaloutput including information associated with at least one property and aspatial distribution of a first set of one or more signals emitted at afirst time point from at least one of a plurality of signal-generatingcomplexes associated with an inner surface of a first skin-coveringmaterial; receiving a second digital output from an image capture deviceat block 1610, the second digital output including informationassociated with at least one property and a spatial distribution of asecond set of one or more signals emitted at a second time point from atleast one of a plurality of signal-generating complexes associated withan inner surface of a second skin-covering material; comparing the firstdigital output with the second digital output at block 1620; generatinga recommended treatment regimen based on the comparison of the firstdigital output with the second digital output at block 1630; andreporting the recommended treatment regimen to a user at block 1640.

In an aspect, the method includes using a first skin-covering materialthat is distinct from the second skin-covering material. For example, afirst skin-covering material can be manufactured for use at the firsttime point and a second skin-covering material manufactured for use atthe second time point. For example, the first skin-covering material caninclude a settable material to generate a first peelable skin-coveringmaterial at the first time point while the second skin-covering materialuses same or different settable material to generate the second peelableskin-covering material at the second time point.

In an aspect, the method includes using a reusable skin-coveringmaterial wherein the plurality of signal-generating complexes on theinner surface of the skin-covering material are refreshed, renewed, orrejuvenated. For example, a pre-formed skin covering material caninclude a removable layer of signal-generating complexes that once usedare removed, e.g., by washing, and a new layer of signal-generatingcomplexes applied to the inner surface. For example, a pre-formed skincovering material can include a renewable layer of signal-generatingcomplexes, wherein a change in pH, heat, or other stimulus is used toremove any bound microbes or parts thereof and to convert thesignal-generating complexes back to a state amenable to interacting withat least one type of microbe and generating a signal accordingly insubsequent uses of the pre-formed skin-covering material. In thismanner, a single, pre-formed skin-covering material can be generated foran individual and used repeatedly with new or refreshedsignal-generating complexes.

In an aspect, the first time point is at a first age of an individualand the second time point is at a second age of an individual. Forexample, the first time point and the second time point may be separatedby days, months, or years depending upon how frequently the skinmicrobiota of an individual is assessed or monitored. In an aspect, thefirst time point is at a time before therapeutic treatment and thesecond time point is at a time after therapeutic treatment. In anaspect, the first time point is at a time point before the onset of apathological condition, e.g., a normal baseline, and the second timepoint is at a time point after the onset of the pathological condition.In an aspect, comparing the microbiota at a first time point versus asecond time point is used to generate a recommended treatment regimen tomaintain and/or modulate the type and spatial distribution of microbeson the skin surface of an individual.

FIG. 17 illustrates aspects of a method for identifying and generating aspatial profile of microbiota of skin. The method includes applying askin-covering material to a skin surface of an individual at block 1700,the skin-covering material including an inner surface and an outersurface, the inner surface substantially conforming in shape to atopography of the skin surface of the individual and including attachedthereto a plurality of signal-generating complexes, one or more of theplurality of signal-generating complexes configured to emit one or moresignals in response to at least one type of microbe; removing theskin-covering material from the skin surface of the individual in block1710; capturing at least one image of the inner surface of theskin-covering material with an image-capture device, the at least oneimage including one or more signals emitted from the one or more of theplurality of signal-generating complexes in response to the at least onetype of microbe and transforming the captured at least one image into adigital output including information associated with at least oneproperty and a spatial distribution of the imaged one or more signals inblock 1720; receiving the digital output from the image-capture devicein block 1730, the digital output including information associated withat least one property and a spatial distribution of the imaged one ormore signals emitted from the one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe; identifying the at least one type of microbe by comparing theinformation associated with the at least one property of the imaged oneor more signals emitted from the one or more of the plurality ofsignal-generating complexes with a database of signal properties ofreference signal-generating complexes in block 1740; generating adigital spatial profile of the at least one type of microbe based on thespatial distribution of the imaged one or more signals emitted from theone or more of the plurality of signal-generating complexes in block1750, and reporting to a user an identification and spatial profile ofthe identified at least one microbe in block 1760.

In an aspect, the method of FIG. 17 includes applying a pre-formedskin-covering material to the skin surface of the individual. In anaspect, the method of FIG. 17 includes applying a settable material tothe skin surface of the individual, the settable material configured toundergo a phase change from a liquid or gelled phase to a flexible solidphase to form a peelable skin-covering material in response to anapplied stimulus. Non-limiting examples of pre-formed and peelableskin-covering material have been described above herein.

In an aspect, applying the skin-covering material to the skin surface ofthe individual includes applying the skin-covering material to the skinsurface of the individual for a prescribed period of time. In an aspect,the prescribed period of time can be one or more seconds. For example,the prescribed period of time may be the time required to press theskin-covering material onto the skin surface and then immediatelyremoving the skin-covering material. For example, the skin-coveringmaterial can be placed in uniform contact with the skin surface andimmediately removed, e.g., about 1-10 seconds. In an aspect, theprescribe period of time can be one or more minutes. For example, theprescribed period of time may be the time required to applyskin-covering material to the skin surface of the individual, followedby additional steps required to aid in capturing the one or moremicrobes from the skin surface. For example, the skin-covering materialcan be placed in uniform contact with the skin surface and allowed tosit on the skin surface for about 10 seconds to about 60 minutes.

In an aspect, applying the skin-covering material to the skin surface ofthe individual includes applying the skin-covering material to the skinsurface of the individual under pressure. For example, pressure may beapplied manually using hands to press the skin-covering material ontothe skin surface of the individual. For example, pressure may be appliedby using a tool that allows for uniform pressing of the skin-coveringmaterial onto the skin surface of the individual.

In an aspect, applying the skin-covering material to the skin surface ofthe individual includes applying the skin-covering material to the skinsurface of the individual in the presence of a vacuum. For example, theskin-covering material may be adhered to the skin, e.g., with anadhesive, and gentle vacuum used to suction microbes from the skinsurface and onto the inner surface of the skin-covering material.

In an aspect, applying the skin-covering material to the skin surface ofthe individual includes applying the skin-covering material to the skinsurface of the individual in the presence of a stimulus. In an aspect,the stimulus includes a thermal or chemical stimulus. For example, theskin surface and/or the skin-covering material may be warmed tofacilitate access to microbes on the skin surface, e.g., by opening skinpores. For example, the skin surface and/or the skin-covering materialmay include a detergent or other agent to aid in removing whole microbesor parts thereof, e.g., proteins, DNA, or RNA, from the skin surface.

FIG. 18 illustrates further aspects of a method such as shown in FIG.17. In an aspect, the method includes applying the plurality ofsignal-generating complexes to the inner surface of the skin-coveringmaterial prior to applying the skin-covering material to the skinsurface of the individual, as shown in block 1800. For example theplurality of signal-generating complexes can be formulated into a spraythat is applied to the inner surface of a pre-formed skin-coveringmaterial prior to applying the skin-covering material to the skinsurface of an individual. For example the plurality of signal-generatingcomplexes can be formulated as a liquid or gel that is applied to theinner surface of a pre-formed skin-covering material prior to applyingthe skin-covering material to the skin surface of an individual. In anaspect, the plurality of signal-generating complexes can be applieddirectly to the skin surface of the individual prior to applying eithera settable material or a pre-formed skin-covering material. For example,the plurality of signal-generating complexes can be modified withstreptavidin to allow binding to a biotin coated inner surface of askin-covering material. In an aspect, the at least one signal-generatingelement and the at least one specific microbe-binding element of asignal-generating complex can be applied separately to the skin surfaceand/or the inner surface of the skin-covering material. For example, asignal-generating element can be modified with biotin and added to theskin surface or directly to an inner surface including a specificmicrobe-binding element modified with avidin.

In an aspect, the method includes separating the skin-covering materialinto one or more pieces along one or more tearable lines of perforation,and capturing at least one image with the image-capture device of theinner surface of at least one of the one or more pieces of theskin-covering material, as shown in block 1810. In an aspect, theskin-covering material can be manufactured with perforations. Forexample, the skin-covering material may be manufactured using athree-dimensional printing process in which the digital template for theskin-covering material includes perforations. In an aspect, theperforations are added to the skin-covering material after manufacture.For example, a skin-covering material manufactured from a thin sheet ofmaterial, e.g., latex or paper may be modified with a device configuredto punch holes through the skin-covering material. In general, thetearable lines of perforation allow the skin-covering material to beseparated into pieces that can be accommodated by the imaging window orscanning surface of the image-capture device. In an aspect, the one ormore tearable lines are configured to allow a non-planar skin-coveringmaterial to be flattened into a planar skin-covering material tofacilitate image analysis, without actually tearing the skin-coveringmaterial into separate pieces.

FIGS. 19A-D illustrate aspects of a method for assessing microbiota ofskin. The method is implemented with a system including skin-coveringmaterial 410, image-capture device 720, and computing device 730. FIG.19A illustrates a cross-section through skin-covering material 410 inproximity to skin surface 1900. Skin-covering material 410 includes apre-formed skin-covering material including inner surface 420 and anouter surface 430, inner surface 420 substantially conforming in shapeto a topography of skin surface 1900. Inner surface 420 includesattached thereto a plurality of signal-generating complexes of a firsttype including signal-generating element of a first type 440 operablycoupled to specific microbe-binding element of a first type 450 and aplurality of signal-generating complexes of a second type includingsignal-generating element of a second type 460 operably coupled tospecific microbe-binding element of a second type 470. Skin surface 1900includes at least one first type of microbe 1910 and at least one secondtype of microbe 1920.

FIG. 19B illustrates applying skin-covering material 410 to skin surface1900. Specific microbe-binding element of a first type 450 recognizes atleast one first type of microbe 1910 while specific microbe-bindingelement of a second type 470 recognizes at least one second type ofmicrobe 1920.

FIG. 19C illustrates removing skin-covering material 410 from skinsurface 1900. At least one first type of microbe 1910 is bound tospecific microbe-binding element of a first type 450 and at least onesecond type of microbe 1920 is bound to specific microbe-binding elementof a second type 470.

FIG. 19D illustrates capturing at least one image of inner surface 420of skin-covering material 410 with image-capture device 720 to image oneor more signals emitted from the one or more of the plurality ofsignal-generating complexes. Signal-generating element of a first type440 emits one or more signals of a first type 1930 in response to the atleast one first type of microbe 1910 bound to operably coupled specificmicrobe-binding element of a first type 450 and signal-generatingelement of a second type 460 emits one or more signals of a second type1940 in response to at the least one second type of microbe 1920 boundto operably coupled specific microbe-binding element of a second type470. In an aspect, the method further includes exposing inner surface420 of skin-covering material 410 with directed energy 750 to elicit asignaling response. The method further includes transforming thecaptured at least one image into a digital output including informationassociated with at least one property and a spatial distribution of theimaged one or more signals.

The method further includes computing device 730 receiving the digitaloutput from image-capture device 720 through communication link 725;identifying the at least one first type of microbe 1910 and the at leastone second type of microbe 1920 by comparing the information associatedwith the at least one property of the one or more signals of a firsttype 1930 and the at least one property of the one or more signals of asecond type 1940 emitted from the one or more of the plurality ofsignal-generating complexes with a database of single properties ofreference signal-generating complexes; generating a digital spatialprofile of the at least one first type of microbe 1910 and the at leastone second type of microbe 1920 based on the spatial distribution of therespective one or more signals of a first type 1930 and one or moresignals of a second type 1940; and reporting to a user an identificationand spatial profile of the identified at least one first type of microbe1910 and at least one second type of microbe 1920.

FIG. 20 illustrates further aspects of a method such as that shown inFIG. 17. In an aspect, the method includes generating a recommendedtreatment regimen based on the identification and the digital spatialprofile of the at least one type of microbe; and reporting therecommended treatment regimen to the user, as shown in block 2000. In anaspect, the method further includes generating a digital alignment ofthe digital spatial profile of the at least one type of microbe with adigital image of the skin surface of the individual covered by the innersurface of the skin-covering material, creating a personalized microbeprofile from the digital alignment, the personalized microbe profileincluding the identification and the spatial profile of the identifiedat least one type of microbe on the skin surface of the individual;generating a recommended treatment regimen based on a comparison of thepersonalized microbe profile with at least one reference microbeprofile; and reporting to the user at least one of the personalizedmicrobe profile or the recommended treatment regimen, as illustrated inblock 2010. For example, a digital image of the individual can becaptured before, during or after placement of the skin-covering materialonto the skin surface. In an aspect, the digital image of theskin-surface of the individual can be used to design a personalizedskin-covering material as described above herein. One or moreregistration marks on the skin-covering material can be used to alignwith one or more landmarks, e.g., moles, blood vessels, or otherlandmarks on the skin surface that are visible in the digital image. Inan aspect, the one or more registration marks are incorporated into themanufacture of the skin-covering material. In an aspect, the one or moreregistration marks can be added, e.g., with a pen or other markingdevice, while the skin-covering material is on the skin-surface of theindividual.

In an aspect, an additional signal-generating element may be applied tothe inner surface of the skin-covering material to enhance the signal ofthe signal-generating complex incorporated into the skin-coveringmaterial or to generate a confirmatory or secondary signaling event. Forexample, an additional signal-generating element may include a vital dyethat intercalates into nucleic acids of captured microbes, non-limitingexamples of which include DAPI (4′,6-diamidino-2-phenylindole), acridineorange, or Hoechst stain. Other non-limiting examples of vital dyesinclude calcein AM, carboxyfluorescein diacetate, DiOC(3,3′-dihexyloxacarbocyanine iodide), rhodamine 123, and Nile red. In anaspect, an additional signal-generating element may include adye-labeled antibody, aptamer, or binding agent that binds to at leastone type of microbe captured by the signal-generating complex. Forexample, the dye-labeled antibody, aptamer, or other binding agent canbind to one or more biomolecule exposed on the outer surface of amicrobe, e.g., a protein, carbohydrate or lipid biomolecule exposed onthe outer surface of the microbe. The label associated with theantibody, aptamer, or other binding agent can include a fluorescentlabel, a colored label, or a chemiluminescent label. For example, thelabeled antibody, aptamer, or other binding agent configured to bind theat least one type of microbe may further include fluorescein for directfluorescence detection or horseradish peroxidase (HRP) for indirectdetection using colorimetric or chemiluminesence following addition ofperoxidase substrate. In some aspects, the labeled antibody, aptamer, orother binding agent configured to bind the at least one type of microbemay further include biotin conjugates available for binding with avidinor streptavidin. In an aspect, the additional signal-generating elementincludes at least one fluorescence-generating agent. In an aspect, theadditional signal-generating element includes at least onechemiluminescence-generating agent. In an aspect, the additionalsignal-generating element includes a dye-labeled anti-16S RNA. In anaspect, the additional signal-generating element includes universalprimers for amplification of microbial 16S gene sequencing the 1.4 kbamplicon and comparing with known sequences in a database, e.g.,Ribosomal Database Project (Cole et al. (2009) Nucl. Acids Res.37(D1):D141-D145; SILVA (Quast et al. (2013) Nucl. Acids Res.41(D1):D590-D596; CORE (“core human oral microbiome;” Griffen et al.(2011), PLoS ONE 6(4):e19051, which are incorporated herein byreference). Other non-limiting examples of the additionalsignal-generating elements include radioactive agents, magnetic agents,radiofrequency identification tags, or contrast agents. In an aspect,the additional signal-generating element can further include labeledoligonucleotides, lectins, proteins, lipids, carbohydrates, ligands, orany other molecule capable carrying a label and interacting with one ormore components of the at least one type of microbe captured on theinner surface of the skin-covering material. In an aspect, theadditional signal-generating element can include one or more of aspecific microbe-binding element, non-limiting examples of which aredescribed below herein. In an aspect, the additional signal-generatingelement can include any one of the signal-generating elements describedabove herein.

FIG. 21 illustrates aspects of a system including a skin-coveringmaterial with perforations and an image-capture device with a feedingmechanism. FIG. 21A illustrates aspects of a skin-covering material2100. Skin-covering material 2100 includes a plurality ofsignal-generating complexes 2110, one or more of the plurality ofsignal-generating complexes 2110 to emit one or more signals in responseto at least one type of microbe. Skin-covering material 2100 furtherincludes one or more tearable perforations 2120. In an aspect, one ormore tearable perforations 2120 are added to the skin-covering materialduring manufacture, e.g., as part of a digital template from which theskin-covering material is manufactured through a 3D-printing process. Inan aspect, one or more tearable perforations 2120 are added to theskin-covering material after manufacture, e.g., by punching a series ofperforations into the skin-covering material. One or more tearableperforations 2120 are configured to separate skin-covering material 2100into segments 2130 a, 2130 b, 2130 c, and 2130 d. Each segment ofskin-covering material 2100 is coded with a corresponding registrationmark 2140 a, 2140 b, 2140 c, and 2140 d. In this example, theregistration marks are represented by a bar code, with each segmenthaving a unique bar code. FIG. 21B illustrates further aspects ofskin-covering material 2100. Skin-covering material 2100 is separableinto segment 2130 d along tearable perforations 2120. Segment 2130 dincludes registration mark 2140 d, the latter of which is used toregister segment 2130 d relative to the other segments of skin-coveringmaterial 2100. In an aspect skin-covering material 2100 including atleast one type of microbe captured by at least one of the plurality ofsignal-generating complexes from a skin surface of an individual isseparated into one or more segments for analysis by an image-capturedevice. FIG. 21C illustrates aspects of a system including skin-coveringmaterial 2100 and image-capture device 2150. Segment 2130 d is fed intofeeding mechanism 2160 of image-capture device 2150. Registration mark2140 d is “read” by a component of image-capture device 2150, e.g., abar code scanner. Additional segments, e.g., 2130 c are separable fromskin-covering material 2100 and can also be subsequently fed intoimage-capture device 2150 for image analysis. The registration mark“read” from each segment is used to align the image information capturedfor each of the segments and aid in compiling a complete image of theentire skin-covering material 2100.

In an aspect, a skin-covering material includes a mouthpiece configuredfor use in a mouth region of an individual. In an aspect, one or moresurfaces of the mouthpiece substantially conform in shape to atopography of at least a portion of the mouth region of the individual.In an aspect, the at least a portion of the mouth region of theindividual includes at least a portion of an oral mucosa, tooth,gingiva, tongue, or palate. For example, the mouthpiece can beconfigured for insertion into a mouth and to cover at least a portion ofan individual's gingiva and teeth. In an aspect, the mouthpiece includesan inner surface defined as those portions of the mouthpiece, e.g., oneor more surfaces of the mouthpiece, in contact with the surfaces of themouth, e.g., the surfaces of the oral mucosa, teeth, gingiva, tongue,and/or palate.

The mouthpiece includes a plurality of signal-generating complexes. Theplurality of signal-generating complexes are associated with one or moresurfaces of the mouthpiece, e.g., one or more inner surfaces in directcontact with one or more surfaces of the mouth region of the individual.The plurality of signal-generating complexes are configured to emit oneor more signals in response to at least one type of microbe, e.g.,bacteria, a virus, a fungus, or a parasite. Non-limiting examples ofbacteria of the oral microbiota include Streptococcus, Actinomyces,Veillonella, Fusobacterium, Porphromonas, Prevotella, Treponema,Nisseria, Haemophilis, Eubacteria, Lactobacterium, Capnocytophaga,Eikenella, Leptotrichia, Peptostreptococcus, Staphylococcus,Corynebacterium, Rothia, Selenomonas, Treponema, Propionibacterium, andTM7 genera 1 and 5. See, e.g., Dewhirst et al. (2010) J. Bacteriology192:5002-5017, which is incorporated herein by reference. Non-limitingexamples of fungi of the oral microbiota include Candida albicans,Aspergillus, Blastomyces dermatitidis, Cryptococcus neoformans, andHistoplasma capsulatum. Non-limiting examples of viruses of the oralmicrobiota include herpes simplex virus (HSV-1), human papillomavirus,coxsackievirus, and Paramyxoviridae viruses. Additional non-limitingexamples of microbes have been described above herein.

In an aspect, the plurality of signal-generating complexes areincorporated into the mouthpiece. In an aspect, the plurality ofsignal-generating complexes are substantially uniformly distributedthroughout the mouthpiece. For example, the plurality ofsignal-generating complexes may be uniformly dispersed in a liquid orgelled form during manufacture of the mouthpiece. In an aspect, theplurality of signal-generating complexes are substantially distributedalong the inner surface of the mouthpiece, e.g., the one or moresurfaces of the mouthpiece substantially conforming in shape to thetopography of the mouth region of the individual. In an aspect, theplurality of signal-generating complexes are functionally attached tothe inner surface of the mouthpiece. In an aspect, the plurality ofsignal-generating complexes are covalently attached to the inner surfaceof the mouthpiece. In an aspect, the plurality of signal-generatingcomplexes are non-covalently attached to the inner surface of themouthpiece.

In an aspect, each of the plurality of signal-generating complexesassociated with the one or more surfaces of the mouthpiece includes atleast one signal-generating element operably and at least one specificmicrobe-binding element. In an aspect, the at least onesignal-generating element is operably coupled to the at least onespecific microbe-binding element, wherein the at least onesignal-generating element is configured to emit one or more signals inresponse to at least one type of microbe bound to the operably coupledat least one specific microbe-binding element. Non-limiting examples ofsignal-generating elements and specific microbe-binding elements havebeen described above herein.

In an aspect, the skin-covering material can include a pre-formedmouthpiece. In an aspect, the pre-formed mouthpiece substantiallyconforms in shape to the topography of at least a portion of the mouthregion of the individual. In an aspect, the pre-formed mouthpiece ispersonalized to substantially conform in shape to the topography of atleast a portion of the mouth region of the individual. For example, adigital three-dimensional representation of the mouth region of theindividual may be used to digitally render a pre-formed mouth piece,which is then used as a template for manufacturing the pre-formedmouthpiece using a three-dimensional printer. In an aspect, thepre-formed mouthpiece is generated using one or more images capturedusing an image-capture device, e.g., a three-dimensional laser scanningsystem, to image the topography of the mouth region of the individual.Non-limiting examples of imaging systems for this purpose include CadentiTero® (from Align Technology, Inc., San Jose, Calif.) and E4D DentistSystem (from ED4 Technologies Richardson, Tex.). Computer-aided designsoftware can be used to generate a digitally rendered model of thepre-formed mouthpiece from which the pre-formed mouthpiece can be formedusing an additive or a subtractive manufacturing process. Non-limitingexamples of modeling programs and manufacturing processes applicable togenerating the pre-formed mouthpiece have been described above herein.

The pre-formed mouthpiece can be formed from any of a number ofmaterials capable of being shaped, molded, or printed. Non-limitingexamples of shapeable, moldable or printable materials include acrylic,nylon, plastic, ceramic, resin, rubber, epoxy, thermoplastic, polymer,photopolymer, polyurethane, gel, hydrogel, latex, or silicone. Othernon-limiting examples of materials have been described above herein.

In an aspect, the skin-covering material can include a peelablemouthpiece. In an aspect, the peelable mouthpiece can include any of anumber of shapeable or moldable materials applied to at least a portionof the mouth region of the individual and subsequently removed, i.e.,peeled, leaving an imprint, wherein the imprint substantially conformsin shape to a topography of the at least one portion of the mouth regionof the individual. In an aspect, the shapeable or moldable material mayharden over an elapsed period of time or in response to exposure to air.In an aspect, the shapeable or moldable material may be hardened inresponse to electromagnetic energy, e.g., light of a specificwavelength, or in response to elevated temperature. In an aspect, thepeelable mouthpiece is formed from a settable material configured toundergo a phase change from a liquid or gelled phase to a flexible solidphase in response to an applied stimulus. The applied stimulus caninclude at least one of exposure to air, a thermal stimulus, or anelectromagnetic stimulus. For example, a peelable mouthpiece can beformed by adding a settable material, e.g., sodium alginate, into animpression tray and inserting the tray with the settable material intothe mouth of the individual and firmly pressing the tray into the teeth.Once the settable material has set, the impression tray including thepeelable mouthpiece is removed from the mouth. Non-limiting settablematerials for use in generating a peelable mouthpiece include sodiumalginate, polyether, silicones, e.g., condensation-cured silicones andaddition-cured silicones, polyvinyl siloxane, agar, or zinc oxideeugenol.

In an aspect, the mouthpiece, whether pre-formed or peelable from asettable material, further includes a medicament for treating a mouthcondition. In an aspect, the medicament can be included as a layer onthe one or more surfaces of the mouthpiece that come in contact with thesurfaces of the mouth region. In an aspect, the medicament can beincorporated into the settable material. In an aspect, the medicamentcan be eluted by simple diffusion from a gel, e.g., a hydrogel,associated with the mouthpiece. Non-limiting examples of medicaments fortreating a mouth condition include antibacterial agents, antifungalagents, antiviral agents, mouth deodorizer, fluoride treatment,probiotics, or prebiotics.

In an aspect, the mouthpiece includes at least one registration mark toregister the mouthpiece to at least one landmark on one or more surfacesof the mouth region of the individual. The one or more landmarks on theone or more surfaces of the mouth region can include pigmented areas,dental topography, oral mucosa texture patterns, blemishes, anatomicalfeatures, or subsurface blood vessels. In an aspect, the one or moreregistration marks are incorporated into the manufacture of themouthpiece based on one or more digital images of the mouth regionincluding the one or more landmarks over which the mouthpiece will beplaced.

In an aspect, the mouthpiece is deformable. In an aspect, the mouthpieceis deformable to facilitate imaging with an image-capture device. Forexample, the mouthpiece may be constructed of a material that is capableof being flattened for the purpose of performing imaging with a scanner,e.g., a flat-bed scanner. In an aspect, the mouthpiece can include oneor more tearable perforations that allow the mouthpiece to be reshapedto facilitate imaging. For example, the mouthpiece can include one ormore tearable or cuttable lines which when torn or cut allow themouthpiece to be in a flattened state.

In an aspect, the mouthpiece is part of a system for assessingmicrobiota of the mouth region. FIG. 22 illustrates aspects of a systemincluding a mouthpiece. System 2200 includes mouthpiece 2210,image-capture device 720, and computing device 730. Mouthpiece 2210 isconfigured for insertion into mouth region 2220 of individual 2230.Mouthpiece 2210 includes an inner surface and an outer surface, whereinthe inner surface includes one or more surfaces of the mouthpiecesubstantially conforming in shape to a topography of mouth region 2220of individual 2230. The inner surface of mouthpiece 2210 includes aplurality of signal-generating complexes. System 2200 further includesimage-capture device 720 including circuitry to capture at least oneimage of the inner surface of mouthpiece 2210 to image one or moresignals 2240 emitted from one or more of the plurality ofsignal-generating complexes and to transform the captured at least oneimage into a digital output including information associated with atleast one property and a spatial distribution of the imaged one or moresignals 2240. In an aspect, one or more signals 2240 are emitted fromthe inner surface of mouthpiece 2210 in response to directed energy 750from image-capture device 720. For example, one or more surfaces ofmouthpiece 2210 can be imaged using a three-dimensional laser scanningsystem.

System 2200 further includes computing device 730 including a processor,computing device 730 operably coupled to image-capture device 720through communications link 725. Computing device 730 includes circuitryconfigured to receive the digital output from image-capture device 720including information associated with the at least one property and thespatial distribution of the imaged one or more signals 2240 emitted fromthe one or more of the plurality of signal-generating complexes inresponse to the at least one type of microbe; compare the properties ofthe imaged one or more signals 2240 emitted from the one or more of theplurality of signal-generating complexes in response to the at least onetype of microbe with a database of emitted signals of referencesignal-generating complexes; and generate a digital spatial profile ofthe at least one type of microbe based on the spatial distribution ofthe imaged one or more signals 2240 emitted from the one or more of theplurality of signal-generating complexes on mouthpiece 2210 in responseto the at least one type of microbe. In an aspect, computing device 730further includes circuitry configured to generate a recommendedtreatment regimen based on a comparison of the generated digital spatialprofile with a reference digital spatial profile. In an aspect,computing device 730 further includes circuitry configured to generate adigital alignment of the generated digital spatial profile with adigital image of one or more surfaces of mouth region 2220 of theindividual 2230 covered by the one or more surfaces of mouthpiece 2210.In an aspect, computing device 730 further includes circuitry togenerate a personalized microbe profile from the generated digitalalignment, the personalized microbe profile including at least one ofthe identity of the at least one type of microbe and a spatialdistribution of the identified at least one type of microbe on the oneor more surfaces of mouth region 2220.

In an aspect, system 2200 further includes at least one of an enhancingcomponent to enhance binding of the at least one type of microbe to oneor more of the plurality of signal-generating complexes associated withthe one or more surfaces of mouthpiece 2210, the at least one enhancingcomponent includes at least one of a thermal component, a vacuumcomponent, a humidity component, a pressure component, a skin-softener,a detergent, or a lysing compound.

In an aspect, the method of assessing microbiota of skin includes amethod of assessing microbiota of the oral cavity. In an aspect, themethod of assessing the microbiota of the oral cavity includes receivinga digital output from an image-capture device, the digital outputincluding information associated with at least one property and aspatial distribution of one or more signals emitted from one or more ofa plurality of signal-generating complexes associated with one or moresurfaces of a mouthpiece, the one or more signals emitted from the oneor more of the plurality of signal-generating complexes in response toat least one type of microbe; identifying the at least one type ofmicrobe by comparing the information associated with at least oneproperty of the one or more signals emitted from the one or more of theplurality of signal-generating complexes with a database of signalproperties of reference signal-generating complexes; generating adigital spatial profile of the at least one type of microbe based on thespatial distribution of the one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to theat least one type of microbe; and reporting to a user an identificationand the digital spatial profile of the identified at least one type ofmicrobe. In an aspect, the method further includes generating arecommended treatment regimen based on the identification and spatialprofile of the at least one type of microbe captured on the surface ofthe mouthpiece; and reporting the recommended treatment regimen to theuser. Non-limiting aspects of a treatment regimen for a mouth regioninclude instructions for brushing techniques; type and use oftoothpaste, fluoride, mouth rinses, flossing, antibacterial agents,anti-fungal agents, antiviral agents, probiotics, or prebiotics; andrecommendation regarding seeing a care provider such as a dentist,periodontist, or oral surgeon.

In an aspect, the method of assessing microbiota of skin includes amethod of assessing microbiota of the oral cavity. In an aspect, themethod of assessing the microbiota of the oral cavity includes applyinga mouthpiece to a mouth region of an individual, the mouthpieceincluding one or more surfaces substantially conforming in shape to atopography of at least a portion of the mouth region of the individual,the one or more surfaces including attached thereto a plurality ofsignal-generating complexes, one or more of the plurality ofsignal-generating complexes configured to emit one or more signals inresponse to at least one type of microbe; removing the mouthpiece fromthe mouth region of the individual; capturing at least one image of theone or more surfaces of the mouthpiece with an image-capture device, theat least one image including one or more signals emitted from one ormore of the plurality of signal-generating complexes in response to theat least one type of microbe and transforming the captured at least oneimage into a digital output including information associated with atleast one property and a spatial distribution of the imaged one or moresignals; receiving the digital output from the image-capture deviceincluding the information associated with at least one property and aspatial distribution of the imaged one or more signals emitted from theone or more of the plurality of signal-generating complexes in responseto the at least one type of microbe; identifying the at least one typeof microbe by comparing the information associated with the at least oneproperty of the imaged one or more signals emitted from the one or moreof the plurality of signal-generating complexes with a database ofsignal properties of reference signal-generating complexes; generating adigital spatial profile of the at least one type of microbe based on thespatial distribution of the imaged one or more signals emitted from theone or more of the plurality of signal-generating complexes; andreporting to a user an identification and a spatial profile of theidentified at least one type of microbe bound to the one or moresurfaces of the mouthpiece. In an aspect, the method further includesgenerating a recommended treatment regimen based on the identificationand the digital spatial profile of the at least one type of microbebound to the one or more surfaces of the mouthpiece; and reporting therecommended treatment regimen to the user. In an aspect, the methodfurther includes generating a digital alignment of the digital spatialprofile of the at least one type of microbe with a digital image of oneor more surfaces of the mouth region of the individual covered by themouthpiece; creating a personalize microbe profile from the digitalalignment, the personalized microbe profile including the identificationand a spatial profile of the identified at least one type of microbe onthe one or more surfaces of the mouth region of the individual;generating a recommended treatment regimen based on the comparison ofthe personalized microbe profile with at least one reference microbeprofile; and reporting to the user at least one of the personalizedmicrobe profile or the recommended treatment regimen.

In an aspect, the method can further include deforming the mouthpiece tofacilitate imaging with the image-capture device. In an aspect,deforming can include separating the mouthpiece into two or more piecesalong one or more lines of tearable or cuttable perforations. In anaspect, deforming can include flattening a malleable non-planarmouthpiece into a substantially planar mouthpiece. In an aspect,deforming can include partially separating the mouthpiece in one or moreplaces to flatten the mouthpiece to facilitate imaging.

In an aspect, the identity and spatial distribution of the at least onetype of microbe on the one or more surfaces of the mouth region of theindividual are indicative of a condition of the oral cavity, e.g.,periodontal disease. For example, the amount of Prevotella at one sitemay indicate developing periodontal disease at that site, whereas anabudance of Prevotella at another site may indicate advanced disease atthe second site. See, e.g., Liu et al. (2012) PLoS ONE 7(6):e37919,which is incorporated herein by reference. In an aspect, the identityand spatial distribution of the at least one type of microbe on the oneor more surfaces of the mouth region of the individual can be used tocorrelate risk with systemic conditions, e.g., cardiovascular disease,preterm birth, stroke, diabetes, pneumonia, or a disease of the centralnervous system. See, e.g., Cockburn, et al. (2012) InvestigativeGenetics 3:19; Dewhirst et al. (2010) J. Bacteriology 192:5002-5017,which are incorporated herein by reference.

In an aspect, the method of assessing microbiota of skin at at least twodifferent time points includes assessing microbiota of a mouth region ofan individual at at least two different time points. In an aspect, themethod includes receiving a first digital output from an image-capturedevice, the first digital output including information associated withat least one property and a spatial distribution of a first set of oneor more signals emitted at a first time point from at least one of aplurality of signal-generating complexes associated with one or moresurfaces of a first mouthpiece; receiving a second digital output fromthe image-capture device, the second digital output includinginformation associated with at least one property and a spatialdistribution of a second set of one or more signals emitted at a secondtime point from at least one of a plurality of signal-generatingcomplexes associated with one or more surfaces of a second mouthpiece;comparing the first digital output with the second digital output;generating a recommended treatment regimen based one comparison of thefirst digital output with the second digital output; and reporting therecommended treatment regimen to a user.

FIG. 23 illustrates aspects of an article of manufacture. Article ofmanufacture 2300 includes non-transitory machine readable media bearingone or more instructions for assessing microbiota of skin in block 2310.The non-transitory machine readable media stores instructions and/ordata for use in assessing microbiota of skin. In an embodiment,non-transitory machine readable media 2310 can be computer readablemedia. In an embodiment, non-transitory machine readable media 2310 canbe recordable-type media. Computer readable media may also berecordable-type media, and the qualities of being “computer readable”and “recordable-type” should not be construed as being mutuallyexclusive, though in some cases a computer readable media may not be arecordable-type media, and vice versa. Machine readable media includevolatile and nonvolatile, removable and non-removable media implementedin any method or technology for storage of information such as machinereadable instructions, data structures, program modules, or other data.Non-transitory machine readable media include, but are not limited to,random-access memory (RAM), read-only memory (ROM), electricallyerasable programmable read-only memory (EEPROM), flash memory, or othermemory technology, CD-ROM, digital versatile disks (DVD), or otheroptical disk storage, magnetic cassettes, magnetic tape, magnetic diskstorage, or other magnetic storage devices, or any other media which canbe used to store the desired information. In a further embodiment,computer storage media may include a group of computer storage mediadevices. In an embodiment, machine readable media may include aninformation store. In an embodiment, an information store may include aquantum memory, a photonic quantum memory, or atomic quantum memory.Combinations of any of the above may also be included within the scopeof non-transitory machine readable media.

Non-transitory machine readable media bearing one or more instructionsfor assessing microbiota of skin, as shown in block 2310, includes oneor more instructions for receiving a digital output from animage-capture device, the digital output including informationassociated with at least one property and a spatial distribution of oneor more signals emitted from one or more of a plurality ofsignal-generating complexes associated with an inner surface of askin-covering material, the one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to atleast one type of microbe in block 2320; one or more instructions forcomparing the information associated with at least one property of theone or more signals emitted from the one or more of the plurality ofsignal-generating complexes with a database of signal properties ofreference signal-generating complexes in block 2330; one or moreinstructions for generating a microbe profile including the at least oneproperty and the spatial distribution of the one or more signals emittedfrom the one or more of the plurality of signal-generating complexes inblock 2340; one or more instructions for generating a recommendedtreatment regimen for an individual based on a comparison of the microbeprofile with a reference microbe profile in block 2350; and one or moreinstructions for reporting to a user at least one of the microbe profileor the recommended treatment regimen in block 2360.

In an aspect, non-transitory machine readable media 2310 can furtherinclude one or more instructions for receiving the digital output fromat least one digital camera. In an aspect, non-transitory machinereadable media 2310 can include one or more instructions for receivingthe digital output from at least one scanning device, wherein thescanning device includes at least one of a passive scanning device, anactive scanning device, a three-dimensional scanning device, an opticalscanning device, a fluorescence scanning device, an acoustic scanningdevice, or an electromagnetic scanning device.

In an aspect, non-transitory machine readable media 2310 can furtherinclude one or more instructions for identifying the at least one typeof microbe by comparing the information associated with the at least oneproperty of the one or more signals emitted from the one or more of theplurality of signal-generating complexes with the database of signalproperties of the reference signal-generating complexes. In an aspect,non-transitory machine readable media 2310 can include one or moreinstructions for comparing the at least one of an optical property,fluorescence property, an infrared emission property, an acousticproperty, a magnetic property, an electromagnetic property, or anelectrical property of the one or more signals emitted from thesignal-generating complex with a database of signal propertiesassociated with one or more reference signal-generating complexes. In anaspect, non-transitory machine readable media 2310 can further includeone or more instructions for comparing at least one of a wavelength, afrequency, or an amplitude of the one or more signals emitted from thesignal-generating complex with a database of signal propertiesassociated with one or more reference signal-generating complexes. In anaspect, the database of signal properties associated with one or morereference signal-generating complexes is included in the article ofmanufacture 2300.

In an aspect, non-transitory machine readable media 2310 includes one ormore instructions for generating a digital spatial profile of the atleast one type of microbe based on the spatial distribution of the oneor more signals emitted from the one or more of the plurality ofsignal-generating complexes. In an aspect, non-transitory machinereadable media 2310 includes one or more instructions for generating adigital alignment of the digital spatial profile of the at least onetype of microbe with a digital image of a skin surface of an individualcovered by the inner surface of the skin-covering material. In anaspect, non-transitory machine readable media 2310 can include one ormore instructions for detecting one or more features depicted in thedigital images, e.g., the physical landmarks, and match these featureswith features in the digital spatial profile, e.g., the registrationmarks. The one or more instructions can include one or more instructionsfor performing feature-based matching using, e.g., segmentation methods,distance transform, affinely invariant neighborhoods, Harris cornerdetection, Maximally Stable External Regions, Canny detector, Laplacianof Gaussian, elastic contour extraction, existing edge detection, lineintersections, local extrema of wavelet transform, inflection points ofcurves, and the like. The one or more instructions may further includeone or more instructions for matching the features detected in the oneor more images of skin surface of the individual with features in thedigital spatial profile using one or more feature-matching methods,non-limiting examples of which include Euclidean distance matching,invariant moments, nearest neighbor based matching, correlation-likemethods, Fourier methods, mutual information methods, optimizationmethods. Further non-limiting examples include methods using spatialrelations, e.g., graph matching algorithms, methods using invariantdescriptors, and relaxation methods.

In an aspect, non-transitory machine readable media 2310 includes one ormore instructions for generating a personalized microbe profile for theindividual from the digital alignment, the personalized microbe profileincluding an identification and a spatial profile of the at least onetype of microbe on the skin surface of the individual; one or moreinstructions for generating the recommended treatment regimen based on acomparison of the personalized microbe profile with the referenceprofile; and one or more instructions for reporting to the user at leastone of the personalized microbe profile or the recommended treatmentregimen. In an aspect, non-transitory machine readable media 2310includes one or more instructions for reporting at least one of thepersonalized microbe profile or the recommended treatment regimen to auser that is the individual for whom the microbiota assessment wasperformed. In an aspect, non-transitory machine readable media 2310includes one or more instructions for reporting at least one of thepersonalized microbe profile or the recommended treatment regimen to auser that is a service provider, e.g., a medical practitioner or otherprovider who is performing the microbiota assessment. In an aspect,non-transitory machine readable media 2310 includes one or moreinstructions providing a visual representation of the personalizedmicrobe profile and/or the recommended treatment regimen to a user on adisplay. In an aspect, non-transitory machine readable media 2310includes one or more instructions for providing a printout to the userof the personalized microbe profile and/or the recommended treatmentregimen. In an aspect, non-transitory machine readable media 2310includes one or more instructions for exporting the personalized microbeprofile and/or the recommended treatment regimen to a computing device,e.g., a second computing device.

In an aspect, non-transitory machine readable media 2310 includes one ormore instructions for generating a recommended treatment regimen basedon comparing microbiota of a skin surface of an individual at two ormore points in time, the one or more instructions including one or moreinstructions for receiving a first digital output from an image-capturedevice, the first digital output including information associated withat least one property and a spatial distribution of a first set of oneor more signal emitted at a first time point from at least one of aplurality of signal-generating complexes associated with an innersurface of a first skin-covering material; one or more instructions forreceiving a second digital output from an image capture device at block,the second digital output including information associated with at leastone property and a spatial distribution of a second set of one or moresignal emitted at a second time point from at least one of a pluralityof signal-generating complexes associated with an inner surface of asecond skin-covering material; one or more instructions for comparingthe first digital output with the second digital; one or moreinstructions for generating a recommended treatment regimen based on thecomparison of the first digital output with the second digital output;and one or more instructions for reporting the recommended treatmentregimen to a user.

In an aspect, non-transitory machine readable media 2310 includes one ormore instructions for comparing the personalized microbe profile with areference microbe profile generated for the individual at a previouspoint in time, e.g., at a young age, before the onset of a skindisorder, or before and/or after a treatment regimen to treat a skindisorder. In an aspect, non-transitory machine readable media 2310includes one or more instructions for comparing the personalized microbeprofile with a reference microbe profile generating for one or moreother individuals, e.g., an average “normal” profile or the profile ofan individual with a desirable microbe profile as exemplified by“healthy” looking skin.

The state of the art has progressed to the point where there is littledistinction left between hardware, software, and/or firmwareimplementations of aspects of systems; the use of hardware, software,and/or firmware is generally (but not always, in that in certaincontexts the choice between hardware and software can becomesignificant) a design choice representing cost vs. efficiency tradeoffs.There are various vehicles by which processes and/or systems and/orother technologies described herein can be effected (e.g., hardware,software, and/or firmware), and that the preferred vehicle will varywith the context in which the processes and/or systems and/or othertechnologies are deployed. For example, if an implementer determinesthat speed and accuracy are paramount, the implementer may opt for amainly hardware and/or firmware vehicle; alternatively, if flexibilityis paramount, the implementer may opt for a mainly softwareimplementation; or, yet again alternatively, the implementer may opt forsome combination of hardware, software, and/or firmware. Hence, thereare several possible vehicles by which the processes and/or devicesand/or other technologies described herein can be effected, none ofwhich is inherently superior to the other in that any vehicle to beutilized is a choice dependent upon the context in which the vehiclewill be deployed and the specific concerns (e.g., speed, flexibility, orpredictability) of the implementer, any of which may vary. Those skilledin the art will recognize that optical aspects of implementations willtypically employ optically-oriented hardware, software, and or firmware.

In some implementations described herein, logic and similarimplementations can include software or other control structures.Electronic circuitry, for example, may have one or more paths ofelectrical current constructed and arranged to implement variousfunctions as described herein. In some implementations, one or moremedia can be configured to bear a device-detectable implementation whensuch media hold or transmit a device detectable instructions operable toperform as described herein. In some variants, for example,implementations can include an update or modification of existingsoftware or firmware, or of gate arrays or programmable hardware, suchas by performing a reception of or a transmission of one or moreinstructions in relation to one or more operations described herein.Alternatively or additionally, in some variants, an implementation caninclude special-purpose hardware, software, firmware components, and/orgeneral-purpose components executing or otherwise invokingspecial-purpose components. Specifications or other implementations canbe transmitted by one or more instances of tangible transmission mediaas described herein, optionally by packet transmission or otherwise bypassing through distributed media at various times.

Alternatively or additionally, implementations may include executing aspecial-purpose instruction sequence or otherwise invoking circuitry forenabling, triggering, coordinating, requesting, or otherwise causing oneor more occurrences of any functional operations described above. Insome variants, operational or other logical descriptions herein may beexpressed directly as source code and compiled or otherwise invoked asan executable instruction sequence. In some contexts, for example, C++or other code sequences can be compiled directly or otherwiseimplemented in high-level descriptor languages (e.g., alogic-synthesizable language, a hardware description language, ahardware design simulation, and/or other such similar mode(s) ofexpression). Alternatively or additionally, some or all of the logicalexpression may be manifested as a Verilog-type hardware description orother circuitry model before physical implementation in hardware,especially for basic operations or timing-critical applications. Thoseskilled in the art will recognize how to obtain, configure, and optimizesuitable transmission or computational elements, material supplies,actuators, or other common structures in light of these teachings.

The foregoing detailed description has set forth various embodiments ofthe devices and/or processes via the use of block diagrams, flowcharts,and/or examples. Insofar as such block diagrams, flowcharts, and/orexamples contain one or more functions and/or operations, it will beunderstood by those within the art that each function and/or operationwithin such block diagrams, flowcharts, or examples can be implemented,individually and/or collectively, by a wide range of hardware, software,firmware, or virtually any combination thereof. In one embodiment,several portions of the subject matter described herein can beimplemented via Application Specific Integrated Circuits (ASICs), FieldProgrammable Gate Arrays (FPGAs), digital signal processors (DSPs), orother integrated formats. However, some aspects of the embodimentsdisclosed herein, in whole or in part, can be equivalently implementedin integrated circuits, as one or more computer programs running on oneor more computers (e.g., as one or more programs running on one or morecomputer systems), as one or more programs running on one or moreprocessors (e.g., as one or more programs running on one or moremicroprocessors), as firmware, or as virtually any combination thereof,and that designing the circuitry and/or writing the code for thesoftware and or firmware would be well within the skill of one of skillin the art in light of this disclosure. In addition, the mechanisms ofthe subject matter described herein are capable of being distributed asa program product in a variety of forms, and that an illustrativeembodiment of the subject matter described herein applies regardless ofthe particular type of signal bearing medium used to actually carry outthe distribution.

In a general sense, those skilled in the art will recognize that thevarious embodiments described herein can be implemented, individuallyand/or collectively, by various types of electro-mechanical systemshaving a wide range of electrical components such as hardware, software,firmware, and/or virtually any combination thereof; and a wide range ofcomponents that may impart mechanical force or motion such as rigidbodies, spring or torsional bodies, hydraulics, electro-magneticallyactuated devices, and/or virtually any combination thereof.Consequently, as used herein “electro-mechanical system” includes, butis not limited to, electrical circuitry operably coupled with atransducer (e.g., an actuator, a motor, a piezoelectric crystal, a MicroElectro Mechanical System (MEMS), etc.), electrical circuitry having atleast one discrete electrical circuit, electrical circuitry having atleast one integrated circuit, electrical circuitry having at least oneapplication specific integrated circuit, electrical circuitry forming ageneral purpose computing device configured by a computer program (e.g.,a general purpose computer configured by a computer program which atleast partially carries out processes and/or devices described herein,or a microprocessor configured by a computer program which at leastpartially carries out processes and/or devices described herein),electrical circuitry forming a memory device (e.g., forms of memory(e.g., random access, flash, read only, etc.)), electrical circuitryforming a communications device (e.g., a modem, communications switch,optical-electrical equipment, etc.), and/or any non-electrical analogthereto, such as optical or other analogs. Those skilled in the art willalso appreciate that examples of electro-mechanical systems include butare not limited to a variety of consumer electronics systems, medicaldevices, as well as other systems such as motorized transport systems,factory automation systems, security systems, and/orcommunication/computing systems. Those skilled in the art will recognizethat electro-mechanical as used herein is not necessarily limited to asystem that has both electrical and mechanical actuation except ascontext may dictate otherwise.

In a general sense, the various aspects described herein can beimplemented, individually and/or collectively, by a wide range ofhardware, software, firmware, and/or any combination thereof and can beviewed as being composed of various types of “electrical circuitry.”Consequently, as used herein “electrical circuitry” includes, but is notlimited to, electrical circuitry having at least one discrete electricalcircuit, electrical circuitry having at least one integrated circuit,electrical circuitry having at least one application specific integratedcircuit, electrical circuitry forming a general purpose computing deviceconfigured by a computer program (e.g., a general purpose computerconfigured by a computer program which at least partially carries outprocesses and/or devices described herein, or a microprocessorconfigured by a computer program which at least partially carries outprocesses and/or devices described herein), electrical circuitry forminga memory device (e.g., forms of memory (e.g., random access, flash, readonly, etc.)), and/or electrical circuitry forming a communicationsdevice (e.g., a modem, communications switch, optical-electricalequipment, etc.). The subject matter described herein can be implementedin an analog or digital fashion or some combination thereof.

Those skilled in the art will recognize that at least a portion of thesystems and/or processes described herein can be integrated into animage processing system. A typical image processing system generallyincludes one or more of a system unit housing, a video display device,memory such as volatile or non-volatile memory, processors such asmicroprocessors or digital signal processors, computational entitiessuch as operating systems, drivers, applications programs, one or moreinteraction devices (e.g., a touch pad, a touch screen, an antenna,etc.), control systems including feedback loops and control motors(e.g., feedback for sensing lens position and/or velocity; controlmotors for moving/distorting lenses to give desired focuses). An imageprocessing system can be implemented utilizing suitable commerciallyavailable components, such as those typically found in digital stillsystems and/or digital motion systems.

Those skilled in the art will recognize that at least a portion of thesystems and/or processes described herein can be integrated into a dataprocessing system. A data processing system generally includes one ormore of a system unit housing, a video display device, memory such asvolatile or non-volatile memory, processors such as microprocessors ordigital signal processors, computational entities such as operatingsystems, drivers, graphical user interfaces, and applications programs,one or more interaction devices (e.g., a touch pad, a touch screen, anantenna, etc.), and/or control systems including feedback loops andcontrol motors (e.g., feedback for sensing position and/or velocity;control motors for moving and/or adjusting components and/orquantities). A data processing system can be implemented utilizingsuitable commercially available components, such as those typicallyfound in data computing/communication and/or networkcomputing/communication systems.

Those skilled in the art will recognize that at least a portion of thesystems and/or processes described herein can be integrated into a motesystem. Those having skill in the art will recognize that a typical motesystem generally includes one or more memories such as volatile ornon-volatile memories, processors such as microprocessors or digitalsignal processors, computational entities such as operating systems,user interfaces, drivers, sensors, actuators, applications programs, oneor more interaction devices (e.g., an antenna USB ports, acoustic ports,etc.), control systems including feedback loops and control motors(e.g., feedback for sensing or estimating position and/or velocity;control motors for moving and/or adjusting components and/orquantities). A mote system may be implemented utilizing suitablecomponents, such as those found in mote computing/communication systems.Specific examples of such components entail such as Intel Corporation'sand/or Crossbow Corporation's mote components and supporting hardware,software, and/or firmware.

In certain cases, use of a system or method may occur in a territoryeven if components are located outside the territory. For example, in adistributed computing context, use of a distributed computing system mayoccur in a territory even though parts of the system may be locatedoutside of the territory (e.g., relay, server, processor, signal-bearingmedium, transmitting computer, receiving computer, etc. located outsidethe territory). A sale of a system or method may likewise occur in aterritory even if components of the system or method are located and/orused outside the territory.

Further, implementation of at least part of a system for performing amethod in one territory does not preclude use of the system in anotherterritory.

One skilled in the art will recognize that the herein describedcomponents (e.g., operations), devices, objects, and the discussionaccompanying them are used as examples for the sake of conceptualclarity and that various configuration modifications are contemplated.Consequently, as used herein, the specific exemplars set forth and theaccompanying discussion are intended to be representative of their moregeneral classes. In general, use of any specific exemplar is intended tobe representative of its class, and the non-inclusion of specificcomponents (e.g., operations), devices, and objects should not be takenlimiting.

With respect to the use of substantially any plural and/or singularterms herein, those having skill in the art can translate from theplural to the singular and/or from the singular to the plural as isappropriate to the context and/or application. The varioussingular/plural permutations are not expressly set forth herein for sakeof clarity.

The herein described subject matter sometimes illustrates differentcomponents contained within, or connected with, different othercomponents. It is to be understood that such depicted architectures aremerely exemplary, and that in fact many other architectures can beimplemented which achieve the same functionality. In a conceptual sense,any arrangement of components to achieve the same functionality iseffectively “associated” such that the desired functionality isachieved. Hence, any two components herein combined to achieve aparticular functionality can be seen as “operably coupled to” each othersuch that the desired functionality is achieved, irrespective ofarchitectures or intermedial components. Likewise, any two components soassociated can also be viewed as being “operably connected,” or“operably coupled,” to each other to achieve the desired functionality,and any two components capable of being so associated can also be viewedas being “operably couplable,” to each other to achieve the desiredfunctionality. Specific examples of operably couplable include but arenot limited to physically mateable and/or physically interactingcomponents, and/or wirelessly interactable, and/or wirelesslyinteracting components, and/or logically interacting, and/or logicallyinteractable components.

In some instances, one or more components can be referred to herein as“configured to,” “configured by,” “configurable to,” “operable/operativeto,” “adapted/adaptable,” “able to,” “conformable/conformed to,” etc.Those skilled in the art will recognize that such terms (e.g.“configured to”) can generally encompass active-state components and/orinactive-state components and/or standby-state components, unlesscontext requires otherwise.

While particular aspects of the present subject matter described hereinhave been shown and described, it will be apparent to those skilled inthe art that, based upon the teachings herein, changes and modificationscan be made without departing from the subject matter described hereinand its broader aspects and, therefore, the appended claims are toencompass within their scope all such changes and modifications as arewithin the true spirit and scope of the subject matter described herein.

It will be understood by those within the art that, in general, termsused herein, and especially in the appended claims (e.g., bodies of theappended claims) are generally intended as “open” terms (e.g., the term“including” should be interpreted as “including but not limited to,” theterm “having” should be interpreted as “having at least,” the term“includes” should be interpreted as “includes but is not limited to,”etc.). It will be further understood by those within the art that if aspecific number of an introduced claim recitation is intended, such anintent will be explicitly recited in the claim, and in the absence ofsuch recitation no such intent is present. For example, as an aid tounderstanding, the following appended claims may contain usage of theintroductory phrases “at least one” and “one or more” to introduce claimrecitations. However, the use of such phrases should not be construed toimply that the introduction of a claim recitation by the indefinitearticles “a” or “an” limits any particular claim containing suchintroduced claim recitation to claims containing only one suchrecitation, even when the same claim includes the introductory phrases“one or more” or “at least one” and indefinite articles such as “a” or“an” (e.g., “a” and/or “an” should typically be interpreted to mean “atleast one” or “one or more”); the same holds true for the use ofdefinite articles used to introduce claim recitations. In addition, evenif a specific number of an introduced claim recitation is explicitlyrecited, those skilled in the art will recognize that such recitationshould typically be interpreted to mean at least the recited number(e.g., the bare recitation of “two recitations,” without othermodifiers, typically means at least two recitations, or two or morerecitations). Furthermore, in those instances where a conventionanalogous to “at least one of A, B, and C, etc.” is used, in generalsuch a construction is intended in the sense one having skill in the artwould understand the convention (e.g., “a system having at least one ofA, B, and C” would include but not be limited to systems that have Aalone, B alone, C alone, A and B together, A and C together, B and Ctogether, and/or A, B, and C together, etc.). In those instances where aconvention analogous to “at least one of A, B, or C, etc.” is used, ingeneral such a construction is intended in the sense one having skill inthe art would understand the convention (e.g., “a system having at leastone of A, B, or C” would include but not be limited to systems that haveA alone, B alone, C alone, A and B together, A and C together, B and Ctogether, and/or A, B, and C together, etc.). It will be furtherunderstood by those within the art that typically a disjunctive wordand/or phrase presenting two or more alternative terms, whether in thedescription, claims, or drawings, should be understood to contemplatethe possibilities of including one of the terms, either of the terms, orboth terms unless context dictates otherwise. For example, the phrase “Aor B” will be typically understood to include the possibilities of “A”or “B” or “A and B.”

Various non-limiting embodiments are described herein as PropheticExamples.

Prophetic Example 1: A Preformed Skin-Covering Material Including aPlurality of Signal-Generating Complexes and Use Thereof

Construction and use of a skin-covering material including a pluralityof signal-generating complexes are described. The skin-covering materialis constructed of a semi-rigid material to substantially conform inshape to the topography of an individual's face. A digitally renderedmodel of the skin-covering material is generated from one or moredigital images of the skin surface of the individual's face. Briefly,two charge-coupled device cameras and a projector connected to acomputer are used to scan the skin surface of the individual's face asdescribed in Feng et al. Brit. J. Oral Maxillofacial Surg. (2010)48:105-109, which is incorporated herein by reference. The individual'sface is exposed to structured light to collect an optical representationof the body region by a point cloud of up to 300,000 points inthree-dimensional coordinates. The three-dimensional coordinates areacquired by the computer and used to construct a digitally renderedmodel of the skin-covering material using a CAD/CAM software package,e.g., Geomagic Studio (Morrisville, N.C.).

The skin-covering material is formed from the digitally rendered modelusing a commercially available 3D printer. An example of a 3D printerappropriate for a physician's office, for example, includes the uPrintSE system (from, e.g., Stratasys, Eden Prairie, Minn.). In this example,software associated with the 3D printer system converts an STL formatfile containing data regarding the digitally rendered model of theskin-covering material into deposition paths that guide the extrusionhead of the printer, printing the skin-covering material layer by layer.The skin-covering material, with an overall thickness of 3 mm, isproduced from a thermoplastic material, e.g., acrylonitrile butadienestyrene (ABS). Several pre-formed skin-covering materials specificallydesigned for the individual can be printed and used at subsequenttreatment appointments. Similarly, the information used to form theskin-covering material can be saved for printing additionalskin-coverings in the future.

The inner surface is further modified with poly(dimethylsiloxane) andcross-linkers to facilitate attachment of oligonucelotides to asubstrate as described in Blank et al. (2003) Proc. Natl. Acad. Sci.,USA. 100:11356-11360, which is incorporated herein by reference.Briefly, the inner surface of the pre-formed skin-covering material iscoated with a thin layer of PDMS (poly(dimethylsiloxane); Sylgard 184,Dow Corning, Midland, Mich.). The PDMS is derivatized with3-aminopropyldimenthylethoxysilane to generate free amino groups towhich a heterobifunctional cross-linking agent, e.g., NHS-PEG-COOH(from, e.g., Pierce, Rockford, Ill.), is attached.

One or more fluorescently labeled aptamers specific for binding at leastone type of microbe, e.g., a bacteria, are generated as described byChen et al. (2007) Biochem. Biophys. Res. Commun. 357:743-748 andJhaveri, et al. (2000) Nature Biotech. 18:1293-1897, which areincorporated herein by reference. The aptamers are designed such thatbinding of a microbe leads to an increase in fluorescence intensity.Briefly, a library of fluorescently labeled oligonucleotides (45-60residues in length) is generated using fluorescein-12-ATP duringsynthesis. The fluorescein-labeled library of oligonucelotides isscreened against whole bacteria, e.g., whole Staphylococcus aureus, inwhich the whole Staphylococcus aureus are incubated with thefluorescein-labeled oligonucleotides, washed, and bound oligonucleotidesare isolated. Those oligonucleotides that bind with high affinity duringthe screening process are further screened for fluorescence signalingproperties in response to binding the target bacteria, e.g., adetectable increase in fluorescein signaling in response to bindingStaphylococcus aureus. The resulting aptamers are further end-modifiedwith an amine group during final synthesis.

The amino-modified, fluorescently labeled aptamer is mixed with across-linker, e.g., ethylene diaminecarbodiimide (EDC), and applied tothe carboxy-modifed inner surface of the skin-covering material. Theskin-covering material is rinsed with a physiological buffer, e.g.,phosphate buffered saline.

The inner surface of the skin-covering material is placed in contactwith the individual's face for 5-10 minutes with manual appliedpressure, e.g., using hands to press the skin-covering material onto theskin surface. The skin-covering material with adhered microbes isremoved from the skin surface and subjected to imaging with animage-capture device.

The inner surface of the skin-covering material is imaged using afluorescence spectrometer including a krypton ion laser, a color CCDcamera, and a long-pass filter (cutoff wavelength, 550 nm) as describedby Koenig & Schneckenburg (in J. Fluorescence (1994) 4:17-40, which isincorporated herein by reference). The excitation wavelength from thekrypton laser is 407 nm. Green fluorescent spots or regionscorresponding to fluorescein-associated fluorescence are imaged usingthe CCD camera.

The spatial distribution of the fluorescent spots or regions captured bythe image-capture device is digitally overlaid with the correspondingdigital image of the individual's face. A color scale may be used tohighlight the abundance of the bacteria detected on the skin surface. Apersonalized microbe profile is generated and includes theidentification and spatial distribution of Staphylococcus aureus on theindividual's face. The personalized microbe profile is provided to theindividual as a printout and accompanied by a recommended treatmentregimen including skin cleansing and use of a nonprescriptiontriple-antibiotic mixture to treat the Staphylococcus aureus infection.

Prophetic Example 2: A Preformed Skin-Covering Material Including aPlurality of Signal-Generating Complexes and Use Thereof

Construction and use of a pre-formed skin-covering material including aplurality of signal-generating complexes are described. A pre-formedskin-covering material is formed using methods such as described inExample 1. In this example, the pre-formed skin-covering material isformed from PMMA (poly(methyl methacrylate)) with a 3D printer (e.g.,Objet Connex 3D printer, from Stratasys Ltd. Minneapolis, Minn.) using adigitally rendered model of an individual's skin surface. The innersurface of the skin-covering material is subjected to reactive ionetching (ME) using an inductively coupled oxygen plasma to generate atextured surface conducive to antibody binding. See, e.g., Rucker et al.(2005) Langmuir 21:7621-7625, which is incorporated herein by reference.

Quantum dot/antibody conjugates are generated against Propionibacteriumacnes using methods described by Dwarakanath et al. (2004) Biochem.Biophys. Res. Commun. 325:739-743, which is incorporated herein byreference. Antibodies to Propionibacterium acnes can be generated fromheat inactivated bacteria as described in Nakatsuji et al. (2008) J.Invest. Dermatol. 127:2451-2457, which is incorporated herein byreference. Fort Orange EviTag quantum dots (about 6 micrograms, fromEvident Technologies, Troy, N.Y.) are modified with the cross-linker EDC(1-ethyl-3-(3-dimethylamino propyl)carbodiimide) in phosphate-bufferedsaline at room temperature for an hour. About 1-2 milligrams of thePropionibacterium acnes antibody are added to the quantum dots, and themixture further incubated for 2 hours. The solution is transferred to aspin filter column apparatus (Omega Macrosep 300k, from Pall, Ann Arbor,Mich.) and spun at 3000 g for 30-60 minutes. The resulting retentatecontains the quantum dot/antibody conjugate.

The textured inner surface of the preformed skin-covering material isincubated with the Propionibacterium acnes quantum dot/antibodyconjugate. The antibodies are prepared in an aqueous solution, e.g.,phosphate buffered saline, and applied in sufficient volume to cover theentirety of the inner surface and allowed to dry for 1 hour. The innersurface is rinsed with phosphate buffered saline supplemented with 0.1%Tween20 to remove non-bound antibody.

The pre-formed skin-covering material including antibodies againstPropionibacterium acnes quantum dot/antibody conjugate is applied to askin surface of an individual to selectively capture these bacteria fromthe skin surface. The skin-covering material is removed from the skinsurface and subjected to fluorescence scanning to detect a shift influorescence associated with Propionibacterium acnes binding to thequantum dot/antibody conjugate. Fort Orange EviTag quantum dotsconjugated to an antibody normally emit at about 600 nm, but emissionfluorescence is shifted to about 450 nm in response to binding theantibody target, e.g., the Propionibacterium acnes. The inner surface ofthe skin-covering material is imaged using a fluorescence spectrometerincluding a krypton ion laser, a color CCD camera, and a long-passfilter (cutoff wavelength, 550 nm) as described by Koenig &Schneckenburg (in J. Fluorescence (1994) 4:17-40, which is incorporatedherein by reference). The excitation wavelength from the krypton laseris 407 nm. Green fluorescent spots or regions corresponding to shiftedfluorescence associated with Fort Orange EviTag quantum dot/antibodyconjugate are imaged using the CCD camera.

The spatial distribution of the fluorescent signal emitted from the FortOrange EviTag quantum dot/antibody conjugate when bound toPropionibacterium acnes is provided to a user as part of a personalizedmicrobe profile the includes a color spatial profile, for example, greenfor Propionibacterium acnes overlaid on an image of the individual'sskin surface. Fluorescent spots or regions captured by the image-capturedevice are digitally overlaid with the corresponding digital image ofthe individual's skin surface using image registration software. A colorscale may be used to highlight the abundance of the bacteria detected atdifferent locations on the skin surface. The personalized microbeprofile is exported to the individual's smart phone and includes arecommended treatment regimen including skin cleansing with gentleliquid cleanser, use of a non-prescription medication containing benzoylperoxide, and recommended non-comedogenic cosmetic brands and/ormoisturizers.

Prophetic Example 3: A Peelable Skin-Covering Material Including aPlurality of Signal-Generating Complexes for Assessing Microbiota ofSkin

Construction and use of a peelable skin-covering material including aplurality of signal-generating complexes are described. The peelableskin-covering material includes a plurality of signal-generatingcomplexes, the signal-generating complexes including at least onebacteria-binding aptamer operably coupled to at least onesignal-generating element, e.g., quantum dots. The bacteria-bindingaptamers are configured to specifically bind Propionibacterium acnes.The aptamers further include quantum dots conjugated to the aptamer andconfigured to fluoresce in response to binding of Propionibacteriumacnes to the bacteria-binding component of the aptamer.

An aptamer that specifically binds Propionibacterium acnes is generatedusing methods described by Chen et al. for generating an aptamer againstbacteria (see Chen et al. (2007) Biochem. Biophys. Res. Commun.357:743-748, which is incorporated herein by reference). Briefly,aptamers against whole Propionibacterium acnes can be isolated from alarge library of 10¹⁴ to 10¹⁵ random oligonucleotides using an iterativein vitro selection procedure (SELEX) in which the whole bacteria areincubated with the oligonucleotides, the washed, and boundoligonucleotides are amplified using the polymerase chain reaction (PCR)method, and then re-incubated with bacteria. One or more aptamers withspecific affinity for Propionibacterium acnes are isolated after 8-10rounds of selection.

A plurality of signal-generating aptamers are formed by modifying theaptamers with a signal-generating element, e.g., quantum dots, asdescribed by Dwarakanath et al. (2004) Biochem. Biophys. Res. Commun.325:739-743, which is incorporated herein by reference. Briefly, theaptamer oligonucleotide sequence is modified by incorporation of 5prime-disulfide primers during the final PCR amplification. Thedisulfide ends are reduced to sulfhydryls in 1% dithiothreitol and the5′-sulfhydryl-aptamers desalted over a Sephadex G-25 column. A linker,e.g., N-beta-maleimidopropionic acid (BMPA, Pierce Biotechnology,Rockford, Ill.) is attached to the sulfhydryl group of the aptamer perthe manufacturer's instructions. The aptamer is conjugated withamine-modified quantum dots (e.g., amine-EviTags, Adirondack Green, fromEvident Technologies, Troy, N.Y.) in the presence of ethylenediaminecarbodiimide (EDC) to generate the signal-generating aptamer.

A settable material, e.g., polyvinyl alcohol, is prepared, mixed withthe plurality of signal-generating aptamers, and applied to a skinsurface of an individual. A peelable skin-covering material is generatedusing polyvinyl alcohol as a settable material using methods such asdescribed in U.S. Pat. No. 5,747,022; U.S. Patent Application2005/0019291, which are incorporated herein by reference. Briefly, for a100 ml solution of settable material, polyvinyl alcohol (10 gm; PVA-523,Sekisui America Corporation, Secaucus, N.J.) is heated in distilledwater at 85° C. for 30 minutes. After cooling, sodium polyacrylate (1.5gm; Rapithix A-60, Ashland Specialty Ingredients, Wayne, N.J.) is addedto the solution along with glycerin (3 gm). Ethanol (10 ml) is added andthe solution volume brought up to 100 ml with distilled water. Theaptamer/quantum dot signal-generating complex is thoroughly mixed intothe cooled polyvinyl alcohol solution just prior to application of thesolution to the skin surface of the individual. The polyvinyl alcoholsolution is applied as in a thin layer to the surface of theindividual's skin and allowed to air dry for 15 to 30 minutes.

Once solidified, one or more registration marks can be added to thepolyvinyl alcohol peelable skin-covering. Registration marks can beplaced on the polyvinyl alcohol peelable skin-covering using ink (e.g.,fluorescent ink) pushed through the outer surface to the inner surfaceof the skin-covering over landmarks on the individual's face, e.g.,freckles, moles, or other markings visible through the translucentgelatin. A digital image of the polyvinyl alcohol peelable skin-coveringon the skin-surface of the individual is also taken to document wherethe landmarks are on the skin surface relative to the registrationmarks. The polyvinyl alcohol peelable skin-covering material is thencarefully peeled from the individual's skin, removing with it microbesassociated with the skin surface.

The polyvinyl alcohol peelable skin-covering including theaptamer/quantum dot signal-generating complex is subjected to imagingwith an image-capture device. Binding of bacteria to an aptamer modifiedwith Adirondack Green quantum dots results in a blue shift, withemission spectra shifting from about 600 nm to about 450 nm when excitedat about 400 nm. See, e.g., described by Dwarakanath et al. (2004)Biochem. Biophys. Res. Commun. 325:739-743, which is incorporated hereinby reference. The inner surface of the skin-covering material is imagedusing a fluorescence spectrometer including a krypton ion laser, a colorCCD camera, and a long-pass filter (cutoff wavelength, 550 nm) asdescribed by Koenig & Schneckenburg (in J. Fluorescence (1994) 4:17-40,which is incorporated herein by reference). The excitation wavelengthfrom the krypton laser is 407 nm. Green fluorescent spots or regionscorresponding to shifted fluorescence associated with Adirondack Greenquantum dot/aptamer conjugate are imaged using the CCD camera.

The spatial distribution of the fluorescent signal emitted from theAdirondack Green quantum dot/aptamer conjugate when bound toPropionibacterium acnes is provided to a user as part of a personalizedmicrobe profile and includes a color spatial profile, for example, greenfor Propionibacterium acnes overlaid on an image of the individual'sskin surface. Fluorescent spots or regions captured by the image-capturedevice are digitally overlaid with the corresponding digital image ofthe individual's skin surface using image registration software. A colorscale may be used to highlight the abundance of the bacteria detected atdifferent locations on the skin surface. The personalized microbeprofile is exported to the individual's smart phone and includes arecommended treatment regimen including skin cleansing with gentleliquid cleanser, use of a non-prescription medication containing benzoylperoxide, and recommended non-comedogenic cosmetic brands and/ormoisturizers.

While various aspects and embodiments have been disclosed herein, otheraspects and embodiments will be apparent to those skilled in the art.The various aspects and embodiments disclosed herein are for purposes ofillustration and are not intended to be limiting, with the true scopeand spirit being indicated by the following claims.

What is claimed is: 1.-59. (canceled)
 60. A system for assessingmicrobiota of skin comprising: an image-capture device includingcircuitry to capture at least one image of an inner surface of theskin-covering material, wherein the skin-covering material includes aninner surface and an outer surface, the inner surface of theskin-covering material substantially conforming in shape to a topographyof a skin surface of an individual and including attached thereto aplurality of signal-generating complexes, one or more of the pluralityof signal-generating complexes configured to emit one or more signals inresponse to at least one type of microbe, and wherein the image includesone or more signals emitted from one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe and to transform the captured at least one image into a digitaloutput including information associated with at least one property and aspatial distribution of the imaged one or more signals; and a computingdevice including a processor, the computing device operably coupled tothe image-capture device and including circuitry configured to receivethe digital output from the image-capture device including theinformation associated with the at least one property and the spatialdistribution of the imaged one or more signals emitted from the one ormore of the plurality of signal-generating complexes in response to theat least one type of microbe; compare the properties of the imaged oneor more signals emitted from the one or more of the plurality ofsignal-generating complexes in response to the at least one type ofmicrobe with a database of emitted signals of referencesignal-generating complexes; and generate a digital spatial profile ofthe at least one type of microbe based on the spatial distribution ofthe imaged one or more signals emitted from the one or more of theplurality of signal-generating complexes in response to the at least onetype of microbe. 61.-63. (canceled)
 64. The system of claim 60, whereinthe skin-covering material includes at least one registration mark toregister the skin-covering material to at least one landmark on the skinsurface of the individual.
 65. (canceled)
 66. The system of claim 60,wherein at least a portion of the inner surface of the skin-coveringmaterial includes a medicament. 67.-79. (canceled)
 80. The system ofclaim 60, wherein the plurality of signal-generating complexes aresubstantially uniformly distributed over at least a portion of the innersurface of the skin-covering material. 81.-83. (canceled)
 84. The systemof claim 60, wherein the skin-covering material includes a plurality ofsignal-generating complexes of at least one first type and a pluralityof signal-generating complexes of at least one second type. 85.(canceled)
 86. The system of claim 84, wherein the plurality ofsignal-generating complexes of the at least one first type areconfigured to emit one or more signals of a first type in response to atleast one first type of microbe and the plurality of signal-generatingcomplexes of the at least one second type are configured to emit one ormore signals of a second type in response to at least one second type ofmicrobe. 87.-89. (canceled)
 90. The system of claim 60, wherein each ofthe plurality of signal-generating complexes includes at least onesignal-generating element and at least one specific microbe-bindingelement. 91.-104. (canceled)
 105. The system of claim 60, wherein theimage-capture device includes at least one scanning device. 106.-109.(canceled)
 110. The system of claim 60, wherein the image-capture deviceincludes at least one of a spectrometer or spectrophotometer. 111.-113.(canceled)
 114. The system of claim 60, wherein the image-capture deviceincludes circuitry configured to capture at least one image of at leastone first portion of the inner surface of the skin-covering material andat least one second portion of the inner surface of the skin-coveringmaterial adjacent to the at least one first portion; and generate acomposite image including the at least one image of the at least onefirst portion of the inner surface of the skin-covering material and theat least one image of the at least one second portion of the innersurface of the skin-covering material.
 115. The system of claim 60,wherein the image-capture device includes a feeding mechanism and animaging surface sized to accommodate at least a portion of theskin-covering material, the feeding mechanism configured to feed in theat least a portion of the skin-covering material onto the imagingsurface. 116.-121. (canceled)
 122. The system of claim 60, wherein thecomputing device includes circuitry configured to compare the generateddigital spatial profile with a reference digital spatial profile. 123.The system of claim 122, wherein the reference digital spatial profileincludes a historical digital spatial profile previously acquired forthe individual.
 124. (canceled)
 125. The system of claim 122, whereinthe computing device includes circuitry configured to generate arecommended treatment regimen based on the comparison of the generateddigital spatial profile with the reference digital spatial profile. 126.The system of claim 60, wherein the computing device includes circuitryconfigured to generate a digital alignment of the generated digitalspatial profile with a digital image of the skin surface of theindividual covered by the inner surface of the skin-covering material.127.-135. (canceled)
 136. The system of claim 60, wherein the computingdevice includes circuitry configured to generate a recommended treatmentregimen based on an identity of the at least one type of microbe and aspatial distribution of the at least one type of microbe on the skinsurface of the individual; and report the generated recommendedtreatment regimen to a user.
 137. The system of claim 60, furthercomprising: at least one enhancing component to enhance interaction ofthe at least one type of microbe to the one or more of the plurality ofsignal-generating complexes. 138.-158. (canceled)
 159. A methodcomprising: receiving a first digital output from an image-capturedevice, the first digital output including information associated withat least one property and a spatial distribution of a first set of oneor more signals emitted at a first time point from at least one of aplurality of signal-generating complexes associated with an innersurface of a first skin-covering material; receiving a second digitaloutput from the image-capture device, the second digital outputincluding information associated with at least one property and aspatial distribution of a second set of one or more signals emitted at asecond time point from at least one of a plurality of signal-generatingcomplexes associated with an inner surface of a second skin-coveringmaterial; comparing the first digital output with the second digitaloutput; generating a recommended treatment regimen based on thecomparison of the first digital output with the second digital output;and reporting the recommended treatment regimen to a user.
 160. A methodcomprising: capturing at least one image of an inner surface of askin-covering material with an image-capture device, wherein theskin-covering material has been removed from a skin surface of anindividual, the inner surface of the skin-covering materialsubstantially conforming in shape to a topography of the skin surface ofthe individual and including attached thereto a plurality ofsignal-generating complexes, one or more of the plurality ofsignal-generating complexes configured to emit one or more signals inresponse to at least one type of microbe, and wherein the at least oneimage includes one or more signals emitted from one or more of theplurality of signal-generating complexes in response to the at least onetype of microbe and transforming the captured at least one image into adigital output including information associated with at least oneproperty and a spatial distribution of the imaged one or more signals;receiving the digital output from the image-capture device, the digitaloutput including information associated with at the least one propertyand the spatial distribution of the imaged one or more signals emittedfrom the one or more of the plurality of signal-generating complexes inresponse to the at least one type of microbe; identifying the at leastone type of microbe by comparing the information associated with the atleast one property of the imaged one or more signals emitted from theone or more of the plurality of signal-generating complexes with adatabase of signal properties of reference signal-generating complexes;generating a digital spatial profile of the at least one type of microbebased on the spatial distribution of the imaged one or more signalsemitted from the one or more of the plurality of signal-generatingcomplexes; and reporting to a user an identification and the digitalspatial profile of the identified at least one type of microbe.161.-168. (canceled)
 169. The method of claim 160, further comprising:generating a digital alignment of the digital spatial profile of the atleast one type of microbe with a digital image of the skin surface ofthe individual covered by the inner surface of the skin-coveringmaterial; creating a personalized microbe profile from the digitalalignment, the personalized microbe profile including the identificationand a spatial profile of the identified at least one type of microbe onthe skin surface of the individual; generating a recommended treatmentregimen based on a comparison of the personalized microbe profile withat least one reference microbe profile; and reporting to the user atleast one of the personalized microbe profile or the recommendedtreatment regimen.
 170. The method of claim 160, further comprising:generating a recommended treatment regimen based on the identificationand the digital spatial profile of the at least one type of microbe; andreporting the recommended treatment regimen to the user. 171.-176.(canceled)